Multiple sequence alignment - TraesCS3B01G146900

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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 TraesCS3B01G146900 chr3B 100.000 5020 0 0 1 5020 136804490 136799471 0.000000e+00 9271.0
1 TraesCS3B01G146900 chr3D 95.117 4690 107 42 1 4615 86940136 86935494 0.000000e+00 7280.0
2 TraesCS3B01G146900 chr3D 92.042 377 6 11 4659 5020 86935511 86935144 4.480000e-140 508.0
3 TraesCS3B01G146900 chr3A 95.646 2848 59 12 1825 4615 103620696 103617857 0.000000e+00 4512.0
4 TraesCS3B01G146900 chr3A 89.163 1541 49 35 257 1720 103622632 103621133 0.000000e+00 1812.0
5 TraesCS3B01G146900 chr3A 91.906 383 3 5 4659 5020 103617874 103617499 1.250000e-140 510.0
6 TraesCS3B01G146900 chr3A 85.507 276 17 6 1 253 103623187 103622912 2.980000e-67 267.0
7 TraesCS3B01G146900 chr3A 95.238 42 1 1 4614 4655 681568680 681568640 1.170000e-06 65.8
8 TraesCS3B01G146900 chr7A 85.472 413 54 4 3571 3980 546262187 546261778 4.650000e-115 425.0
9 TraesCS3B01G146900 chr7A 83.761 234 35 2 1047 1280 546263809 546263579 8.460000e-53 219.0
10 TraesCS3B01G146900 chr7A 81.579 190 33 2 3270 3458 546262545 546262357 6.730000e-34 156.0
11 TraesCS3B01G146900 chr7D 83.688 423 61 5 3562 3980 450245478 450245060 4.710000e-105 392.0
12 TraesCS3B01G146900 chr7D 83.333 198 27 6 3264 3458 450245815 450245621 1.440000e-40 178.0
13 TraesCS3B01G146900 chr7B 83.688 423 61 5 3562 3980 468406089 468405671 4.710000e-105 392.0
14 TraesCS3B01G146900 chr7B 82.745 255 38 5 1029 1280 468407679 468407428 6.540000e-54 222.0
15 TraesCS3B01G146900 chr7B 90.370 135 13 0 3270 3404 468406409 468406275 1.440000e-40 178.0
16 TraesCS3B01G146900 chr6D 89.510 143 15 0 3262 3404 149304718 149304860 1.110000e-41 182.0
17 TraesCS3B01G146900 chr6B 86.713 143 19 0 3262 3404 262275172 262275314 5.200000e-35 159.0
18 TraesCS3B01G146900 chr2A 76.498 217 44 6 1066 1280 84944386 84944175 1.480000e-20 111.0
19 TraesCS3B01G146900 chr5B 97.619 42 1 0 4615 4656 70560896 70560855 6.970000e-09 73.1


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 TraesCS3B01G146900 chr3B 136799471 136804490 5019 True 9271.000000 9271 100.0000 1 5020 1 chr3B.!!$R1 5019
1 TraesCS3B01G146900 chr3D 86935144 86940136 4992 True 3894.000000 7280 93.5795 1 5020 2 chr3D.!!$R1 5019
2 TraesCS3B01G146900 chr3A 103617499 103623187 5688 True 1775.250000 4512 90.5555 1 5020 4 chr3A.!!$R2 5019
3 TraesCS3B01G146900 chr7A 546261778 546263809 2031 True 266.666667 425 83.6040 1047 3980 3 chr7A.!!$R1 2933
4 TraesCS3B01G146900 chr7D 450245060 450245815 755 True 285.000000 392 83.5105 3264 3980 2 chr7D.!!$R1 716
5 TraesCS3B01G146900 chr7B 468405671 468407679 2008 True 264.000000 392 85.6010 1029 3980 3 chr7B.!!$R1 2951

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
824 1170 0.040351 CCTCTCCTCTCACCTCACCA 59.960 60.0 0.00 0.00 0.00 4.17 F
1323 1713 0.469917 TCCATGGCCTTGCTAGCTAC 59.530 55.0 17.23 2.33 0.00 3.58 F
2125 2861 0.468585 ATGTACCCATGCCATGCCAG 60.469 55.0 0.00 0.00 0.00 4.85 F
2899 3688 0.520847 GCAAGGCAGTCTTCAAGCTC 59.479 55.0 0.00 0.00 32.41 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 2862 0.535102 ACAAGGCACCAGGAGAAACG 60.535 55.0 0.0 0.0 0.00 3.60 R
3244 4086 0.179048 CATTCACGCTGATGGGGCTA 60.179 55.0 0.0 0.0 0.00 3.93 R
3502 4360 0.118346 TTTCTGGGAGGAGGCTGGTA 59.882 55.0 0.0 0.0 0.00 3.25 R
4699 5602 0.105760 TGGCACACCATTTGTTCCCT 60.106 50.0 0.0 0.0 40.64 4.20 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
52 53 3.184628 TGAGATGAGATGAAACCCCACT 58.815 45.455 0.00 0.00 0.00 4.00
76 81 1.168714 CAGCCCCTCAAAAGCTACAC 58.831 55.000 0.00 0.00 34.38 2.90
77 82 0.771127 AGCCCCTCAAAAGCTACACA 59.229 50.000 0.00 0.00 34.38 3.72
111 116 4.887071 TGCTGCTGTAAAAGGAGAGAAAAA 59.113 37.500 0.00 0.00 46.96 1.94
116 121 4.134563 TGTAAAAGGAGAGAAAAAGCGCT 58.865 39.130 2.64 2.64 0.00 5.92
159 164 1.308047 GACTGACATGCCACACAACA 58.692 50.000 0.00 0.00 0.00 3.33
161 166 1.023502 CTGACATGCCACACAACACA 58.976 50.000 0.00 0.00 0.00 3.72
198 213 5.123820 GCAGAGCACAAGGATAATTACACAA 59.876 40.000 0.00 0.00 0.00 3.33
204 219 7.394359 AGCACAAGGATAATTACACAAACAGAT 59.606 33.333 0.00 0.00 0.00 2.90
206 221 9.988350 CACAAGGATAATTACACAAACAGATAC 57.012 33.333 0.00 0.00 0.00 2.24
207 222 9.959721 ACAAGGATAATTACACAAACAGATACT 57.040 29.630 0.00 0.00 0.00 2.12
307 607 1.890979 GCGGCATGTCCATCAGAGG 60.891 63.158 0.00 0.00 34.01 3.69
308 608 1.227764 CGGCATGTCCATCAGAGGG 60.228 63.158 0.00 0.00 34.01 4.30
309 609 1.150081 GGCATGTCCATCAGAGGGG 59.850 63.158 0.07 0.00 34.01 4.79
310 610 1.348008 GGCATGTCCATCAGAGGGGA 61.348 60.000 0.07 0.00 34.01 4.81
311 611 0.108207 GCATGTCCATCAGAGGGGAG 59.892 60.000 0.07 0.00 32.85 4.30
313 613 0.344790 ATGTCCATCAGAGGGGAGGT 59.655 55.000 0.07 0.00 32.85 3.85
355 663 1.407258 GAATCCTCTCTGTAGCACGCT 59.593 52.381 0.00 0.00 0.00 5.07
431 747 2.256306 TGGAACAGTGCTATCACAGGA 58.744 47.619 0.00 0.00 45.49 3.86
470 790 1.826487 GGCTCGAGGGAGAGAGACC 60.826 68.421 15.58 0.00 43.27 3.85
496 818 3.871594 GAGAGAAAGGTCGAGAGAGAGAG 59.128 52.174 0.00 0.00 43.49 3.20
499 821 5.365605 AGAGAAAGGTCGAGAGAGAGAGATA 59.634 44.000 0.00 0.00 43.49 1.98
501 823 5.365605 AGAAAGGTCGAGAGAGAGAGATAGA 59.634 44.000 0.00 0.00 43.49 1.98
503 825 3.578716 AGGTCGAGAGAGAGAGATAGAGG 59.421 52.174 0.00 0.00 43.49 3.69
504 826 3.323979 GGTCGAGAGAGAGAGATAGAGGT 59.676 52.174 0.00 0.00 43.49 3.85
506 828 4.038763 GTCGAGAGAGAGAGATAGAGGTGA 59.961 50.000 0.00 0.00 43.49 4.02
508 830 4.280929 CGAGAGAGAGAGATAGAGGTGAGA 59.719 50.000 0.00 0.00 0.00 3.27
615 937 1.485838 GCTCGCTCCACATCACATCG 61.486 60.000 0.00 0.00 0.00 3.84
641 980 4.863925 GTCTCGCTCTCGGCAGCC 62.864 72.222 0.00 0.00 41.91 4.85
823 1169 0.333312 TCCTCTCCTCTCACCTCACC 59.667 60.000 0.00 0.00 0.00 4.02
824 1170 0.040351 CCTCTCCTCTCACCTCACCA 59.960 60.000 0.00 0.00 0.00 4.17
825 1171 1.181786 CTCTCCTCTCACCTCACCAC 58.818 60.000 0.00 0.00 0.00 4.16
826 1172 0.609406 TCTCCTCTCACCTCACCACG 60.609 60.000 0.00 0.00 0.00 4.94
986 1363 7.169982 GGATATACATACATAGAATTGAGCGGC 59.830 40.741 0.00 0.00 0.00 6.53
1006 1383 1.430632 CTGTTGGTGCGGATGATGC 59.569 57.895 0.00 0.00 0.00 3.91
1289 1677 8.836268 AAGAAAATCTACGGTAAACACATACA 57.164 30.769 0.00 0.00 0.00 2.29
1290 1678 8.248117 AGAAAATCTACGGTAAACACATACAC 57.752 34.615 0.00 0.00 0.00 2.90
1299 1689 4.525100 GGTAAACACATACACCCAACCATT 59.475 41.667 0.00 0.00 0.00 3.16
1318 1708 3.518766 CCATTCCATGGCCTTGCTA 57.481 52.632 13.15 3.48 44.70 3.49
1320 1710 0.672342 CATTCCATGGCCTTGCTAGC 59.328 55.000 13.15 8.10 0.00 3.42
1321 1711 0.554792 ATTCCATGGCCTTGCTAGCT 59.445 50.000 17.23 0.00 0.00 3.32
1322 1712 1.212375 TTCCATGGCCTTGCTAGCTA 58.788 50.000 17.23 7.59 0.00 3.32
1323 1713 0.469917 TCCATGGCCTTGCTAGCTAC 59.530 55.000 17.23 2.33 0.00 3.58
1324 1714 0.471617 CCATGGCCTTGCTAGCTACT 59.528 55.000 17.23 0.00 0.00 2.57
1325 1715 1.694150 CCATGGCCTTGCTAGCTACTA 59.306 52.381 17.23 0.87 0.00 1.82
1326 1716 2.548920 CCATGGCCTTGCTAGCTACTAC 60.549 54.545 17.23 4.39 0.00 2.73
1327 1717 1.120530 TGGCCTTGCTAGCTACTACC 58.879 55.000 17.23 11.33 0.00 3.18
1328 1718 1.343075 TGGCCTTGCTAGCTACTACCT 60.343 52.381 17.23 0.00 0.00 3.08
1329 1719 1.763545 GGCCTTGCTAGCTACTACCTT 59.236 52.381 17.23 0.00 0.00 3.50
1330 1720 2.483889 GGCCTTGCTAGCTACTACCTTG 60.484 54.545 17.23 0.00 0.00 3.61
1331 1721 2.483889 GCCTTGCTAGCTACTACCTTGG 60.484 54.545 17.23 5.19 0.00 3.61
1332 1722 3.031736 CCTTGCTAGCTACTACCTTGGA 58.968 50.000 17.23 0.00 0.00 3.53
1333 1723 3.068873 CCTTGCTAGCTACTACCTTGGAG 59.931 52.174 17.23 0.00 0.00 3.86
1334 1724 3.383698 TGCTAGCTACTACCTTGGAGT 57.616 47.619 17.23 0.00 0.00 3.85
1335 1725 3.709587 TGCTAGCTACTACCTTGGAGTT 58.290 45.455 17.23 0.00 0.00 3.01
1336 1726 3.447586 TGCTAGCTACTACCTTGGAGTTG 59.552 47.826 17.23 0.00 0.00 3.16
1337 1727 3.447944 GCTAGCTACTACCTTGGAGTTGT 59.552 47.826 7.70 0.00 0.00 3.32
1338 1728 4.440387 GCTAGCTACTACCTTGGAGTTGTC 60.440 50.000 7.70 0.00 0.00 3.18
1339 1729 3.780626 AGCTACTACCTTGGAGTTGTCT 58.219 45.455 0.00 0.00 0.00 3.41
1383 1773 1.610522 TCTGCTTCTTCCTTTGCTTGC 59.389 47.619 0.00 0.00 0.00 4.01
1543 1936 3.363844 AAGAGAGAAGAGCGGCGGC 62.364 63.158 9.78 8.43 40.37 6.53
1544 1937 4.135153 GAGAGAAGAGCGGCGGCA 62.135 66.667 19.21 0.00 43.41 5.69
1545 1938 4.140599 AGAGAAGAGCGGCGGCAG 62.141 66.667 19.21 0.00 43.41 4.85
1746 2139 1.205460 AGGTGGCCACGGGTCTATTT 61.205 55.000 29.08 3.51 0.00 1.40
1753 2147 1.656652 CACGGGTCTATTTCCTGCTG 58.343 55.000 0.00 0.00 34.93 4.41
1896 2621 1.227645 CGACGCCATCCACATCCAT 60.228 57.895 0.00 0.00 0.00 3.41
1991 2723 8.272545 TGCTTATAGTACTAGTCGTTCTTCAA 57.727 34.615 8.85 0.00 0.00 2.69
2007 2739 7.494625 TCGTTCTTCAAACTGTAACTCATCTTT 59.505 33.333 0.00 0.00 0.00 2.52
2071 2803 1.334869 GCCACCTTGCTGTATGTATGC 59.665 52.381 0.00 0.00 0.00 3.14
2076 2808 4.577693 CACCTTGCTGTATGTATGCATCTT 59.422 41.667 0.19 0.00 36.55 2.40
2125 2861 0.468585 ATGTACCCATGCCATGCCAG 60.469 55.000 0.00 0.00 0.00 4.85
2126 2862 2.123769 TACCCATGCCATGCCAGC 60.124 61.111 0.00 0.00 0.00 4.85
2238 3000 4.022416 GTCTGTATTTTTGTGCCCATGTCA 60.022 41.667 0.00 0.00 0.00 3.58
2487 3276 2.408022 GACCGCTACGAGTCGCAT 59.592 61.111 13.59 0.00 0.00 4.73
2599 3388 5.144456 CCACATGGAGAACCTCAAGGTCA 62.144 52.174 1.33 0.00 42.62 4.02
2899 3688 0.520847 GCAAGGCAGTCTTCAAGCTC 59.479 55.000 0.00 0.00 32.41 4.09
3044 3838 6.937392 TGCATAGTAACATAACCTGTGTGTA 58.063 36.000 0.00 0.00 38.39 2.90
3255 4097 2.203209 GCCGGTTAGCCCCATCAG 60.203 66.667 1.90 0.00 0.00 2.90
3262 4104 0.546122 TTAGCCCCATCAGCGTGAAT 59.454 50.000 0.00 0.00 34.64 2.57
3502 4360 4.678574 CGCACATTTCCACCATCATTTCAT 60.679 41.667 0.00 0.00 0.00 2.57
3554 4412 3.267597 GACCGCGTGCTGCCAATTT 62.268 57.895 4.92 0.00 42.08 1.82
3752 4652 3.485346 GACCCAGTTCAACCCGGCA 62.485 63.158 0.00 0.00 0.00 5.69
4425 5328 0.889186 GTTCTTTGGCAAGGGCGAGA 60.889 55.000 9.63 1.90 42.47 4.04
4439 5342 1.001158 GGCGAGAGGATAAACGGAGAG 60.001 57.143 0.00 0.00 0.00 3.20
4440 5343 1.001158 GCGAGAGGATAAACGGAGAGG 60.001 57.143 0.00 0.00 0.00 3.69
4455 5358 2.039879 GGAGAGGGGCAAAAAGAGTACA 59.960 50.000 0.00 0.00 0.00 2.90
4582 5485 5.468072 CGATGCAGAGTAGAAGCCATTAAAT 59.532 40.000 0.00 0.00 0.00 1.40
4615 5518 3.334891 ACTGGGTGCGGGCCATTA 61.335 61.111 4.39 0.00 0.00 1.90
4616 5519 2.828549 CTGGGTGCGGGCCATTAC 60.829 66.667 4.39 0.00 0.00 1.89
4617 5520 4.434354 TGGGTGCGGGCCATTACC 62.434 66.667 4.39 9.15 0.00 2.85
4626 5529 0.821517 GGGCCATTACCGAAAAAGGG 59.178 55.000 4.39 0.00 35.02 3.95
4627 5530 1.552578 GGCCATTACCGAAAAAGGGT 58.447 50.000 0.00 0.00 41.62 4.34
4628 5531 1.897133 GGCCATTACCGAAAAAGGGTT 59.103 47.619 0.00 0.00 38.99 4.11
4629 5532 2.300723 GGCCATTACCGAAAAAGGGTTT 59.699 45.455 0.00 0.00 38.99 3.27
4630 5533 3.581755 GCCATTACCGAAAAAGGGTTTC 58.418 45.455 0.00 0.00 38.99 2.78
4631 5534 3.615592 GCCATTACCGAAAAAGGGTTTCC 60.616 47.826 0.00 0.00 38.99 3.13
4632 5535 3.056393 CCATTACCGAAAAAGGGTTTCCC 60.056 47.826 0.00 0.00 45.90 3.97
4642 5545 3.850508 GGTTTCCCCACGCTTTGT 58.149 55.556 0.00 0.00 0.00 2.83
4643 5546 3.024431 GGTTTCCCCACGCTTTGTA 57.976 52.632 0.00 0.00 0.00 2.41
4644 5547 1.541379 GGTTTCCCCACGCTTTGTAT 58.459 50.000 0.00 0.00 0.00 2.29
4645 5548 1.890489 GGTTTCCCCACGCTTTGTATT 59.110 47.619 0.00 0.00 0.00 1.89
4646 5549 3.083293 GGTTTCCCCACGCTTTGTATTA 58.917 45.455 0.00 0.00 0.00 0.98
4647 5550 3.119743 GGTTTCCCCACGCTTTGTATTAC 60.120 47.826 0.00 0.00 0.00 1.89
4648 5551 3.420300 TTCCCCACGCTTTGTATTACA 57.580 42.857 0.00 0.00 0.00 2.41
4649 5552 3.420300 TCCCCACGCTTTGTATTACAA 57.580 42.857 5.14 5.14 36.11 2.41
4650 5553 3.752665 TCCCCACGCTTTGTATTACAAA 58.247 40.909 18.39 18.39 44.91 2.83
4693 5596 3.578688 CATTTAAGAGTGCCTTGCCAAC 58.421 45.455 0.00 0.00 36.34 3.77
4694 5597 2.656947 TTAAGAGTGCCTTGCCAACT 57.343 45.000 0.00 0.00 36.34 3.16
4695 5598 1.896220 TAAGAGTGCCTTGCCAACTG 58.104 50.000 0.00 0.00 36.34 3.16
4696 5599 1.458639 AAGAGTGCCTTGCCAACTGC 61.459 55.000 0.00 0.00 41.77 4.40
4697 5600 2.914097 AGTGCCTTGCCAACTGCC 60.914 61.111 0.00 0.00 40.16 4.85
4698 5601 3.225798 GTGCCTTGCCAACTGCCA 61.226 61.111 0.00 0.00 40.16 4.92
4699 5602 2.443577 TGCCTTGCCAACTGCCAA 60.444 55.556 0.00 0.00 40.16 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.544683 TCTCATCTCATCAGTCATCACCT 58.455 43.478 0.00 0.00 0.00 4.00
52 53 1.075482 CTTTTGAGGGGCTGCCTGA 59.925 57.895 19.68 0.00 0.00 3.86
127 132 4.216257 GCATGTCAGTCAGGTTGTTATGTT 59.784 41.667 0.00 0.00 0.00 2.71
159 164 4.240103 TGCTCCGCACTGTGCTGT 62.240 61.111 28.04 0.00 42.25 4.40
161 166 3.586461 CTCTGCTCCGCACTGTGCT 62.586 63.158 28.04 0.00 42.25 4.40
198 213 7.550551 CACTCATTCATGTTGGTAGTATCTGTT 59.449 37.037 0.00 0.00 0.00 3.16
204 219 5.419542 GCTCACTCATTCATGTTGGTAGTA 58.580 41.667 0.00 0.00 0.00 1.82
206 221 3.308053 CGCTCACTCATTCATGTTGGTAG 59.692 47.826 0.00 0.00 0.00 3.18
207 222 3.261580 CGCTCACTCATTCATGTTGGTA 58.738 45.455 0.00 0.00 0.00 3.25
208 223 2.079158 CGCTCACTCATTCATGTTGGT 58.921 47.619 0.00 0.00 0.00 3.67
209 224 1.202110 GCGCTCACTCATTCATGTTGG 60.202 52.381 0.00 0.00 0.00 3.77
291 591 1.150081 CCCCTCTGATGGACATGCC 59.850 63.158 0.01 0.00 37.10 4.40
307 607 2.607750 TCAGCACCCTCACCTCCC 60.608 66.667 0.00 0.00 0.00 4.30
308 608 1.194781 TTCTCAGCACCCTCACCTCC 61.195 60.000 0.00 0.00 0.00 4.30
309 609 0.036858 GTTCTCAGCACCCTCACCTC 60.037 60.000 0.00 0.00 0.00 3.85
310 610 0.764369 TGTTCTCAGCACCCTCACCT 60.764 55.000 0.00 0.00 0.00 4.00
311 611 0.321122 CTGTTCTCAGCACCCTCACC 60.321 60.000 0.00 0.00 34.79 4.02
313 613 0.972134 CTCTGTTCTCAGCACCCTCA 59.028 55.000 0.00 0.00 41.10 3.86
421 729 0.387202 CTCCTGGCGTCCTGTGATAG 59.613 60.000 0.00 0.00 0.00 2.08
431 747 1.077625 AACCTCTCTCTCCTGGCGT 59.922 57.895 0.00 0.00 0.00 5.68
470 790 1.668751 CTCTCGACCTTTCTCTCTCCG 59.331 57.143 0.00 0.00 0.00 4.63
496 818 3.914426 TTTGGCCTTCTCACCTCTATC 57.086 47.619 3.32 0.00 0.00 2.08
499 821 1.543429 CGTTTTGGCCTTCTCACCTCT 60.543 52.381 3.32 0.00 0.00 3.69
501 823 0.472471 TCGTTTTGGCCTTCTCACCT 59.528 50.000 3.32 0.00 0.00 4.00
503 825 2.616842 TCTTTCGTTTTGGCCTTCTCAC 59.383 45.455 3.32 0.00 0.00 3.51
504 826 2.878406 CTCTTTCGTTTTGGCCTTCTCA 59.122 45.455 3.32 0.00 0.00 3.27
506 828 3.208747 TCTCTTTCGTTTTGGCCTTCT 57.791 42.857 3.32 0.00 0.00 2.85
508 830 3.020984 TGTTCTCTTTCGTTTTGGCCTT 58.979 40.909 3.32 0.00 0.00 4.35
615 937 0.657840 GAGAGCGAGACAGAGAGAGC 59.342 60.000 0.00 0.00 0.00 4.09
641 980 3.676216 GGGGGCACAACGGTAAAG 58.324 61.111 0.00 0.00 0.00 1.85
823 1169 3.036084 GGAGACGTGGTGTGCGTG 61.036 66.667 0.00 0.00 43.04 5.34
1289 1677 2.469952 CATGGAATGGAATGGTTGGGT 58.530 47.619 0.00 0.00 41.79 4.51
1318 1708 3.764972 GAGACAACTCCAAGGTAGTAGCT 59.235 47.826 0.00 0.00 37.19 3.32
1320 1710 5.712917 AGAAGAGACAACTCCAAGGTAGTAG 59.287 44.000 0.00 0.00 43.53 2.57
1321 1711 5.642165 AGAAGAGACAACTCCAAGGTAGTA 58.358 41.667 0.00 0.00 43.53 1.82
1322 1712 4.484912 AGAAGAGACAACTCCAAGGTAGT 58.515 43.478 0.00 0.00 43.53 2.73
1323 1713 5.474825 GAAGAAGAGACAACTCCAAGGTAG 58.525 45.833 0.00 0.00 43.53 3.18
1324 1714 4.022242 CGAAGAAGAGACAACTCCAAGGTA 60.022 45.833 0.00 0.00 43.53 3.08
1325 1715 3.243907 CGAAGAAGAGACAACTCCAAGGT 60.244 47.826 0.00 0.00 43.53 3.50
1326 1716 3.243907 ACGAAGAAGAGACAACTCCAAGG 60.244 47.826 0.00 0.00 43.53 3.61
1327 1717 3.983741 ACGAAGAAGAGACAACTCCAAG 58.016 45.455 0.00 0.00 43.53 3.61
1328 1718 3.637229 AGACGAAGAAGAGACAACTCCAA 59.363 43.478 0.00 0.00 43.53 3.53
1329 1719 3.223435 AGACGAAGAAGAGACAACTCCA 58.777 45.455 0.00 0.00 43.53 3.86
1330 1720 3.926821 AGACGAAGAAGAGACAACTCC 57.073 47.619 0.00 0.00 43.53 3.85
1331 1721 4.022676 AGGAAGACGAAGAAGAGACAACTC 60.023 45.833 0.00 0.00 42.90 3.01
1332 1722 3.892588 AGGAAGACGAAGAAGAGACAACT 59.107 43.478 0.00 0.00 0.00 3.16
1333 1723 4.231439 GAGGAAGACGAAGAAGAGACAAC 58.769 47.826 0.00 0.00 0.00 3.32
1334 1724 3.058155 CGAGGAAGACGAAGAAGAGACAA 60.058 47.826 0.00 0.00 0.00 3.18
1335 1725 2.484651 CGAGGAAGACGAAGAAGAGACA 59.515 50.000 0.00 0.00 0.00 3.41
1336 1726 2.159490 CCGAGGAAGACGAAGAAGAGAC 60.159 54.545 0.00 0.00 0.00 3.36
1337 1727 2.085320 CCGAGGAAGACGAAGAAGAGA 58.915 52.381 0.00 0.00 0.00 3.10
1338 1728 1.468395 GCCGAGGAAGACGAAGAAGAG 60.468 57.143 0.00 0.00 0.00 2.85
1339 1729 0.526662 GCCGAGGAAGACGAAGAAGA 59.473 55.000 0.00 0.00 0.00 2.87
1383 1773 1.734465 GTCGTTGGGAGATCAAGCAAG 59.266 52.381 0.00 0.00 0.00 4.01
1723 2116 2.528378 ACCCGTGGCCACCTAACT 60.528 61.111 29.95 5.34 0.00 2.24
1879 2604 2.350522 GATATGGATGTGGATGGCGTC 58.649 52.381 0.00 0.00 0.00 5.19
1896 2621 1.078214 GGCAGCACAGCAGTGGATA 60.078 57.895 11.54 0.00 45.98 2.59
1991 2723 5.941788 ACCCAAGAAAGATGAGTTACAGTT 58.058 37.500 0.00 0.00 0.00 3.16
2007 2739 2.819608 GCTGCAAAACTATGACCCAAGA 59.180 45.455 0.00 0.00 0.00 3.02
2071 2803 7.605410 AGAAAAATGCAGGCATAAAAAGATG 57.395 32.000 7.26 0.00 35.31 2.90
2076 2808 8.580720 TGTAAGTAGAAAAATGCAGGCATAAAA 58.419 29.630 7.26 0.00 35.31 1.52
2125 2861 1.600916 AAGGCACCAGGAGAAACGC 60.601 57.895 0.00 0.00 0.00 4.84
2126 2862 0.535102 ACAAGGCACCAGGAGAAACG 60.535 55.000 0.00 0.00 0.00 3.60
2127 2863 0.954452 CACAAGGCACCAGGAGAAAC 59.046 55.000 0.00 0.00 0.00 2.78
2128 2864 0.823356 GCACAAGGCACCAGGAGAAA 60.823 55.000 0.00 0.00 43.97 2.52
2312 3098 1.838396 AGGCAAGCAAACAAGGGGG 60.838 57.895 0.00 0.00 0.00 5.40
2899 3688 3.200593 GCCATGAGCTGCGTCTGG 61.201 66.667 11.46 11.46 38.99 3.86
3036 3830 2.923655 CTGGATGCGTAAGTACACACAG 59.076 50.000 0.00 0.00 41.68 3.66
3044 3838 2.699954 CAAGAACCTGGATGCGTAAGT 58.300 47.619 0.00 0.00 41.68 2.24
3244 4086 0.179048 CATTCACGCTGATGGGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
3255 4097 0.647410 CTCCACGATGTCATTCACGC 59.353 55.000 0.00 0.00 0.00 5.34
3262 4104 1.184970 TGCACTCCTCCACGATGTCA 61.185 55.000 0.00 0.00 0.00 3.58
3502 4360 0.118346 TTTCTGGGAGGAGGCTGGTA 59.882 55.000 0.00 0.00 0.00 3.25
3550 4408 0.678048 GCCGAGCTGTCAGGGAAATT 60.678 55.000 1.14 0.00 0.00 1.82
3554 4412 2.685017 ATGCCGAGCTGTCAGGGA 60.685 61.111 1.14 0.00 0.00 4.20
4198 5098 9.967346 ATTATATGTTAGTGCAGTACAGTACAG 57.033 33.333 13.37 6.12 33.80 2.74
4291 5194 5.221244 CGAAAAGGACAGAAAAACTTGGGAT 60.221 40.000 0.00 0.00 0.00 3.85
4425 5328 0.326238 TGCCCCTCTCCGTTTATCCT 60.326 55.000 0.00 0.00 0.00 3.24
4439 5342 2.820197 CCTCTTGTACTCTTTTTGCCCC 59.180 50.000 0.00 0.00 0.00 5.80
4440 5343 3.751518 TCCTCTTGTACTCTTTTTGCCC 58.248 45.455 0.00 0.00 0.00 5.36
4455 5358 3.454082 CTCTCATACCTGCCTTTCCTCTT 59.546 47.826 0.00 0.00 0.00 2.85
4582 5485 0.325933 CAGTGGTGCCCATCTCTTCA 59.674 55.000 0.00 0.00 35.28 3.02
4597 5500 3.636929 TAATGGCCCGCACCCAGTG 62.637 63.158 0.00 0.00 35.48 3.66
4598 5501 3.334891 TAATGGCCCGCACCCAGT 61.335 61.111 0.00 0.00 35.48 4.00
4599 5502 2.828549 GTAATGGCCCGCACCCAG 60.829 66.667 0.00 0.00 35.48 4.45
4600 5503 4.434354 GGTAATGGCCCGCACCCA 62.434 66.667 0.00 0.00 36.66 4.51
4602 5505 3.980442 TTCGGTAATGGCCCGCACC 62.980 63.158 0.00 3.15 45.09 5.01
4603 5506 1.587933 TTTTCGGTAATGGCCCGCAC 61.588 55.000 0.00 0.00 45.09 5.34
4604 5507 0.894184 TTTTTCGGTAATGGCCCGCA 60.894 50.000 0.00 0.00 45.09 5.69
4605 5508 0.179148 CTTTTTCGGTAATGGCCCGC 60.179 55.000 0.00 0.00 45.09 6.13
4606 5509 0.454196 CCTTTTTCGGTAATGGCCCG 59.546 55.000 0.00 0.00 46.83 6.13
4607 5510 0.821517 CCCTTTTTCGGTAATGGCCC 59.178 55.000 0.00 0.00 0.00 5.80
4608 5511 1.552578 ACCCTTTTTCGGTAATGGCC 58.447 50.000 0.00 0.00 0.00 5.36
4609 5512 3.581755 GAAACCCTTTTTCGGTAATGGC 58.418 45.455 0.00 0.00 31.69 4.40
4610 5513 4.182693 GGAAACCCTTTTTCGGTAATGG 57.817 45.455 0.00 0.00 31.69 3.16
4625 5528 7.005424 TTGTAATACAAAGCGTGGGGAAACC 62.005 44.000 2.97 0.00 42.37 3.27
4626 5529 3.502979 TGTAATACAAAGCGTGGGGAAAC 59.497 43.478 0.00 0.00 0.00 2.78
4627 5530 3.752665 TGTAATACAAAGCGTGGGGAAA 58.247 40.909 0.00 0.00 0.00 3.13
4628 5531 3.420300 TGTAATACAAAGCGTGGGGAA 57.580 42.857 0.00 0.00 0.00 3.97
4629 5532 3.420300 TTGTAATACAAAGCGTGGGGA 57.580 42.857 2.97 0.00 34.76 4.81
4638 5541 4.024725 AGCGTCGTTGCTTTGTAATACAAA 60.025 37.500 16.57 16.57 44.46 2.83
4639 5542 3.495377 AGCGTCGTTGCTTTGTAATACAA 59.505 39.130 1.08 1.08 44.46 2.41
4640 5543 3.061322 AGCGTCGTTGCTTTGTAATACA 58.939 40.909 0.00 0.00 44.46 2.29
4641 5544 3.404564 CAGCGTCGTTGCTTTGTAATAC 58.595 45.455 0.00 0.00 44.46 1.89
4642 5545 2.413796 CCAGCGTCGTTGCTTTGTAATA 59.586 45.455 3.21 0.00 44.46 0.98
4643 5546 1.196808 CCAGCGTCGTTGCTTTGTAAT 59.803 47.619 3.21 0.00 44.46 1.89
4644 5547 0.584396 CCAGCGTCGTTGCTTTGTAA 59.416 50.000 3.21 0.00 44.46 2.41
4645 5548 1.225376 CCCAGCGTCGTTGCTTTGTA 61.225 55.000 3.21 0.00 44.46 2.41
4646 5549 2.542907 CCCAGCGTCGTTGCTTTGT 61.543 57.895 3.21 0.00 44.46 2.83
4647 5550 2.252260 CCCAGCGTCGTTGCTTTG 59.748 61.111 3.21 0.00 44.46 2.77
4648 5551 2.203153 ACCCAGCGTCGTTGCTTT 60.203 55.556 3.21 0.00 44.46 3.51
4649 5552 2.972505 CACCCAGCGTCGTTGCTT 60.973 61.111 3.21 0.00 44.46 3.91
4693 5596 1.001181 CACCATTTGTTCCCTTGGCAG 59.999 52.381 0.00 0.00 32.26 4.85
4694 5597 1.047002 CACCATTTGTTCCCTTGGCA 58.953 50.000 0.00 0.00 32.26 4.92
4695 5598 1.047801 ACACCATTTGTTCCCTTGGC 58.952 50.000 0.00 0.00 33.09 4.52
4696 5599 1.270252 GCACACCATTTGTTCCCTTGG 60.270 52.381 0.00 0.00 35.67 3.61
4697 5600 1.270252 GGCACACCATTTGTTCCCTTG 60.270 52.381 0.00 0.00 35.57 3.61
4698 5601 1.047801 GGCACACCATTTGTTCCCTT 58.952 50.000 0.00 0.00 35.57 3.95
4699 5602 0.105760 TGGCACACCATTTGTTCCCT 60.106 50.000 0.00 0.00 40.64 4.20
4719 5624 2.949106 CCGTGCTTGCTCCAACTG 59.051 61.111 0.00 0.00 0.00 3.16
4720 5625 2.980233 GCCGTGCTTGCTCCAACT 60.980 61.111 0.00 0.00 0.00 3.16
4809 5720 1.466856 CACACCACCATTGCTATGCT 58.533 50.000 2.27 0.00 0.00 3.79
4925 5848 0.833287 AGTGGTGAGTGACAGCTTGT 59.167 50.000 0.00 0.00 45.86 3.16


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

AutoCloner maintained by Alex Coulton.