Multiple sequence alignment - TraesCS4B01G064500

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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 TraesCS4B01G064500 chr4B 100.000 2358 0 0 1 2358 57529015 57531372 0.000000e+00 4355.0
1 TraesCS4B01G064500 chr4B 86.418 1259 69 41 321 1505 57272763 57271533 0.000000e+00 1284.0
2 TraesCS4B01G064500 chr4B 79.564 367 55 14 994 1350 57741213 57741569 6.510000e-61 244.0
3 TraesCS4B01G064500 chr4B 76.903 381 44 25 977 1350 57744391 57744734 2.410000e-40 176.0
4 TraesCS4B01G064500 chr4A 84.472 1829 161 55 3 1764 561107049 561105277 0.000000e+00 1690.0
5 TraesCS4B01G064500 chr4A 81.513 357 45 14 996 1351 560998483 560998147 8.300000e-70 274.0
6 TraesCS4B01G064500 chr4A 77.803 437 64 22 926 1350 561072259 561071844 3.030000e-59 239.0
7 TraesCS4B01G064500 chr4D 83.238 1581 131 53 3 1518 39272799 39274310 0.000000e+00 1328.0
8 TraesCS4B01G064500 chr4D 83.288 371 40 17 985 1351 39365980 39365628 2.920000e-84 322.0
9 TraesCS4B01G064500 chr4D 77.677 439 67 22 926 1350 39336073 39336494 3.030000e-59 239.0
10 TraesCS4B01G064500 chr4D 77.844 334 64 9 1 327 69345222 69345552 5.140000e-47 198.0
11 TraesCS4B01G064500 chr7B 95.575 565 24 1 1793 2357 222315089 222315652 0.000000e+00 904.0
12 TraesCS4B01G064500 chr7B 93.993 566 31 3 1793 2358 51061318 51061880 0.000000e+00 854.0
13 TraesCS4B01G064500 chr1B 95.053 566 28 0 1793 2358 585830226 585829661 0.000000e+00 891.0
14 TraesCS4B01G064500 chr1B 93.640 566 35 1 1793 2358 624018103 624017539 0.000000e+00 845.0
15 TraesCS4B01G064500 chr3B 94.180 567 30 3 1793 2358 426087098 426086534 0.000000e+00 861.0
16 TraesCS4B01G064500 chr3B 94.180 567 30 3 1793 2358 428201252 428200688 0.000000e+00 861.0
17 TraesCS4B01G064500 chr5B 94.004 567 31 3 1793 2358 700597574 700598138 0.000000e+00 856.0
18 TraesCS4B01G064500 chr5B 76.301 173 35 5 1594 1764 554752086 554752254 1.160000e-13 87.9
19 TraesCS4B01G064500 chrUn 93.827 567 31 4 1793 2358 31720082 31720645 0.000000e+00 850.0
20 TraesCS4B01G064500 chr2B 93.640 566 35 1 1793 2358 60962372 60961808 0.000000e+00 845.0
21 TraesCS4B01G064500 chr2A 85.992 514 41 11 1215 1715 541387022 541386527 2.690000e-144 521.0
22 TraesCS4B01G064500 chr3D 78.743 334 63 6 1 330 350859085 350858756 1.420000e-52 217.0
23 TraesCS4B01G064500 chr2D 77.545 334 65 9 1 327 476475028 476475358 2.390000e-45 193.0
24 TraesCS4B01G064500 chr5A 77.485 342 62 13 1 330 278355146 278354808 8.600000e-45 191.0
25 TraesCS4B01G064500 chr7A 76.627 338 65 13 1 330 680755309 680754978 8.660000e-40 174.0
26 TraesCS4B01G064500 chr1A 81.522 184 30 4 147 327 465128111 465128293 5.250000e-32 148.0
27 TraesCS4B01G064500 chr1D 78.082 146 22 9 155 290 27944238 27944383 1.500000e-12 84.2


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 TraesCS4B01G064500 chr4B 57529015 57531372 2357 False 4355 4355 100.0000 1 2358 1 chr4B.!!$F1 2357
1 TraesCS4B01G064500 chr4B 57271533 57272763 1230 True 1284 1284 86.4180 321 1505 1 chr4B.!!$R1 1184
2 TraesCS4B01G064500 chr4B 57741213 57744734 3521 False 210 244 78.2335 977 1350 2 chr4B.!!$F2 373
3 TraesCS4B01G064500 chr4A 561105277 561107049 1772 True 1690 1690 84.4720 3 1764 1 chr4A.!!$R3 1761
4 TraesCS4B01G064500 chr4D 39272799 39274310 1511 False 1328 1328 83.2380 3 1518 1 chr4D.!!$F1 1515
5 TraesCS4B01G064500 chr7B 222315089 222315652 563 False 904 904 95.5750 1793 2357 1 chr7B.!!$F2 564
6 TraesCS4B01G064500 chr7B 51061318 51061880 562 False 854 854 93.9930 1793 2358 1 chr7B.!!$F1 565
7 TraesCS4B01G064500 chr1B 585829661 585830226 565 True 891 891 95.0530 1793 2358 1 chr1B.!!$R1 565
8 TraesCS4B01G064500 chr1B 624017539 624018103 564 True 845 845 93.6400 1793 2358 1 chr1B.!!$R2 565
9 TraesCS4B01G064500 chr3B 426086534 426087098 564 True 861 861 94.1800 1793 2358 1 chr3B.!!$R1 565
10 TraesCS4B01G064500 chr3B 428200688 428201252 564 True 861 861 94.1800 1793 2358 1 chr3B.!!$R2 565
11 TraesCS4B01G064500 chr5B 700597574 700598138 564 False 856 856 94.0040 1793 2358 1 chr5B.!!$F2 565
12 TraesCS4B01G064500 chrUn 31720082 31720645 563 False 850 850 93.8270 1793 2358 1 chrUn.!!$F1 565
13 TraesCS4B01G064500 chr2B 60961808 60962372 564 True 845 845 93.6400 1793 2358 1 chr2B.!!$R1 565

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
250 261 0.033208 TCCATGGCCCAAAGACCATC 60.033 55.0 6.96 0.0 44.97 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 3980 0.039888 TGTGACGCGAGATCAAACGA 60.04 50.0 15.93 0.0 0.0 3.85 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
31 33 1.670791 GAAGGACAACACCGACCAAA 58.329 50.000 0.00 0.00 34.73 3.28
33 35 1.892209 AGGACAACACCGACCAAATC 58.108 50.000 0.00 0.00 34.73 2.17
44 46 0.179084 GACCAAATCCCGCGAGATCA 60.179 55.000 8.23 0.00 0.00 2.92
45 47 0.469917 ACCAAATCCCGCGAGATCAT 59.530 50.000 8.23 0.00 0.00 2.45
46 48 0.870393 CCAAATCCCGCGAGATCATG 59.130 55.000 8.23 8.56 0.00 3.07
47 49 1.586422 CAAATCCCGCGAGATCATGT 58.414 50.000 8.23 0.00 0.00 3.21
49 51 0.250038 AATCCCGCGAGATCATGTGG 60.250 55.000 8.23 9.24 35.50 4.17
55 57 1.269465 CGCGAGATCATGTGGAGACAT 60.269 52.381 0.00 0.00 46.14 3.06
58 60 3.858877 GCGAGATCATGTGGAGACATACC 60.859 52.174 0.00 0.00 46.14 2.73
112 115 5.052693 CATAGGGATGGGATCAAACTTGA 57.947 43.478 0.00 0.00 42.14 3.02
128 131 8.367660 TCAAACTTGAGAGACATTACTCCTAT 57.632 34.615 0.00 0.00 37.60 2.57
131 134 7.118496 ACTTGAGAGACATTACTCCTATTGG 57.882 40.000 0.00 0.00 37.60 3.16
134 137 5.148502 GAGAGACATTACTCCTATTGGGGA 58.851 45.833 0.00 0.00 37.25 4.81
162 165 1.602323 TCGCCACACAACCCCAATC 60.602 57.895 0.00 0.00 0.00 2.67
186 190 3.254166 AGACGCTAAACCTAACAAGACGA 59.746 43.478 0.00 0.00 0.00 4.20
193 197 1.546476 ACCTAACAAGACGAGAGCAGG 59.454 52.381 0.00 0.00 0.00 4.85
195 199 0.246635 TAACAAGACGAGAGCAGGGC 59.753 55.000 0.00 0.00 0.00 5.19
227 231 4.856607 CGAGCCGAGGTCCTTCGC 62.857 72.222 0.00 0.00 39.19 4.70
250 261 0.033208 TCCATGGCCCAAAGACCATC 60.033 55.000 6.96 0.00 44.97 3.51
256 267 0.749454 GCCCAAAGACCATCGCAGAT 60.749 55.000 0.00 0.00 45.12 2.90
258 269 1.679944 CCCAAAGACCATCGCAGATGT 60.680 52.381 14.50 5.88 45.12 3.06
298 309 1.306226 ACGGGAGGAGGAGGAAAGG 60.306 63.158 0.00 0.00 0.00 3.11
306 317 2.248686 AGGAGGAGGAAAGGCTGAGATA 59.751 50.000 0.00 0.00 0.00 1.98
314 327 7.127955 AGGAGGAAAGGCTGAGATATTTTCTTA 59.872 37.037 0.00 0.00 33.74 2.10
316 329 8.688747 AGGAAAGGCTGAGATATTTTCTTATG 57.311 34.615 0.00 0.00 33.74 1.90
327 340 9.853177 GAGATATTTTCTTATGGAGGAGGAAAA 57.147 33.333 0.00 0.00 39.23 2.29
400 418 2.237143 TCGAAGCAGTGAATCTCCCATT 59.763 45.455 0.00 0.00 0.00 3.16
452 470 8.462016 GCAGCTCTAGAAATAAAGAATGGAAAA 58.538 33.333 0.00 0.00 0.00 2.29
529 549 6.364435 GCAAGATAAGTTTTCAAGCTCAAAGG 59.636 38.462 0.00 0.00 0.00 3.11
604 642 0.462789 GGTACGTCAACCCGATCCAT 59.537 55.000 0.00 0.00 33.02 3.41
880 963 0.601311 GCGGCACAAAGTCAGAGAGT 60.601 55.000 0.00 0.00 0.00 3.24
909 992 1.663739 CAGCATGCAGTTTGGCTGT 59.336 52.632 21.98 0.00 46.47 4.40
932 1035 1.902508 TGAACTGAAGCCTCCCTGTAG 59.097 52.381 0.00 0.00 0.00 2.74
964 1067 2.098298 CGCGCTGCAACCACATAC 59.902 61.111 5.56 0.00 0.00 2.39
965 1068 2.676029 CGCGCTGCAACCACATACA 61.676 57.895 5.56 0.00 0.00 2.29
967 1070 1.013596 GCGCTGCAACCACATACATA 58.986 50.000 0.00 0.00 0.00 2.29
968 1071 1.603802 GCGCTGCAACCACATACATAT 59.396 47.619 0.00 0.00 0.00 1.78
976 1079 2.479837 ACCACATACATATTCGCACGG 58.520 47.619 0.00 0.00 0.00 4.94
1064 3276 3.958798 CTCTCCGGTAAGTCCATCCTTAA 59.041 47.826 0.00 0.00 35.57 1.85
1097 3309 1.272784 CGCTTCAACGACGCACAGTA 61.273 55.000 0.00 0.00 34.06 2.74
1098 3310 1.068474 GCTTCAACGACGCACAGTAT 58.932 50.000 0.00 0.00 0.00 2.12
1099 3311 1.059264 GCTTCAACGACGCACAGTATC 59.941 52.381 0.00 0.00 0.00 2.24
1100 3312 2.596452 CTTCAACGACGCACAGTATCT 58.404 47.619 0.00 0.00 0.00 1.98
1101 3313 1.977188 TCAACGACGCACAGTATCTG 58.023 50.000 0.00 0.00 37.52 2.90
1102 3314 1.538075 TCAACGACGCACAGTATCTGA 59.462 47.619 3.70 0.00 35.18 3.27
1103 3315 1.649171 CAACGACGCACAGTATCTGAC 59.351 52.381 3.70 0.00 35.18 3.51
1104 3316 0.179197 ACGACGCACAGTATCTGACG 60.179 55.000 3.70 8.97 39.19 4.35
1105 3317 1.464429 CGACGCACAGTATCTGACGC 61.464 60.000 3.70 5.13 37.80 5.19
1106 3318 0.179161 GACGCACAGTATCTGACGCT 60.179 55.000 3.70 0.00 37.80 5.07
1107 3319 0.243907 ACGCACAGTATCTGACGCTT 59.756 50.000 3.70 0.00 37.80 4.68
1108 3320 0.917259 CGCACAGTATCTGACGCTTC 59.083 55.000 3.70 0.00 35.18 3.86
1109 3321 1.732405 CGCACAGTATCTGACGCTTCA 60.732 52.381 3.70 0.00 35.18 3.02
1110 3322 2.337583 GCACAGTATCTGACGCTTCAA 58.662 47.619 3.70 0.00 35.18 2.69
1111 3323 2.092838 GCACAGTATCTGACGCTTCAAC 59.907 50.000 3.70 0.00 35.18 3.18
1112 3324 3.317150 CACAGTATCTGACGCTTCAACA 58.683 45.455 3.70 0.00 35.18 3.33
1113 3325 3.740832 CACAGTATCTGACGCTTCAACAA 59.259 43.478 3.70 0.00 35.18 2.83
1154 3371 5.564651 GCTTTATCCTTGCTTGTGTTTGCTA 60.565 40.000 0.00 0.00 0.00 3.49
1418 3650 4.517523 GCTCAATAAAGCTGCATGTGTGC 61.518 47.826 1.02 1.71 41.16 4.57
1448 3684 4.873827 TGGAGTAAGTAACGAATGGAATGC 59.126 41.667 0.00 0.00 0.00 3.56
1449 3685 5.116882 GGAGTAAGTAACGAATGGAATGCT 58.883 41.667 0.00 0.00 0.00 3.79
1499 3735 5.856156 TGCAATCCATTGATCAAGTTTTGT 58.144 33.333 14.54 0.00 40.14 2.83
1500 3736 6.990798 TGCAATCCATTGATCAAGTTTTGTA 58.009 32.000 14.54 10.95 40.14 2.41
1501 3737 6.867816 TGCAATCCATTGATCAAGTTTTGTAC 59.132 34.615 14.54 1.08 40.14 2.90
1526 3762 4.096003 GCTAAGCACCGGCCAGGA 62.096 66.667 18.74 0.00 45.00 3.86
1569 3805 6.917217 AGAAAGAACTGAGAAAACACAGAG 57.083 37.500 0.00 0.00 37.54 3.35
1591 3827 0.178961 AGCTCAGTTTTTGGACCCCC 60.179 55.000 0.00 0.00 0.00 5.40
1592 3828 0.178961 GCTCAGTTTTTGGACCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
1593 3829 1.074889 GCTCAGTTTTTGGACCCCCTA 59.925 52.381 0.00 0.00 0.00 3.53
1594 3830 2.490168 GCTCAGTTTTTGGACCCCCTAA 60.490 50.000 0.00 0.00 0.00 2.69
1598 3834 3.699538 CAGTTTTTGGACCCCCTAATAGC 59.300 47.826 0.00 0.00 0.00 2.97
1607 3843 0.600255 CCCCTAATAGCTGGCGAACG 60.600 60.000 0.00 0.00 0.00 3.95
1608 3844 0.104304 CCCTAATAGCTGGCGAACGT 59.896 55.000 0.00 0.00 0.00 3.99
1609 3845 1.488527 CCTAATAGCTGGCGAACGTC 58.511 55.000 0.00 0.00 0.00 4.34
1635 3874 2.092995 CGACGGATAACATTTGCGAACA 59.907 45.455 0.00 0.00 0.00 3.18
1640 3879 5.571357 ACGGATAACATTTGCGAACATTTTC 59.429 36.000 0.00 0.00 0.00 2.29
1661 3900 3.055530 TCCTTGGCAGATTCTTCAGAGAC 60.056 47.826 0.00 0.00 0.00 3.36
1666 3905 3.491619 GGCAGATTCTTCAGAGACGCATA 60.492 47.826 0.00 0.00 0.00 3.14
1667 3906 4.115516 GCAGATTCTTCAGAGACGCATAA 58.884 43.478 0.00 0.00 0.00 1.90
1671 3910 5.982516 AGATTCTTCAGAGACGCATAACATC 59.017 40.000 0.00 0.00 0.00 3.06
1685 3924 5.578336 CGCATAACATCTTCTTCAGAGACAA 59.422 40.000 0.00 0.00 33.87 3.18
1689 3928 9.159364 CATAACATCTTCTTCAGAGACAAATGA 57.841 33.333 0.00 0.00 33.87 2.57
1690 3929 7.432350 AACATCTTCTTCAGAGACAAATGAC 57.568 36.000 0.00 0.00 33.87 3.06
1691 3930 6.528321 ACATCTTCTTCAGAGACAAATGACA 58.472 36.000 0.00 0.00 33.87 3.58
1692 3931 6.649973 ACATCTTCTTCAGAGACAAATGACAG 59.350 38.462 0.00 0.00 33.87 3.51
1693 3932 6.166984 TCTTCTTCAGAGACAAATGACAGT 57.833 37.500 0.00 0.00 0.00 3.55
1694 3933 6.586344 TCTTCTTCAGAGACAAATGACAGTT 58.414 36.000 0.00 0.00 0.00 3.16
1695 3934 7.050377 TCTTCTTCAGAGACAAATGACAGTTT 58.950 34.615 0.00 0.00 0.00 2.66
1711 3950 7.889873 TGACAGTTTCTGGGAAGAATAAAAA 57.110 32.000 1.90 0.00 35.51 1.94
1714 3953 9.764363 GACAGTTTCTGGGAAGAATAAAAATTT 57.236 29.630 1.90 0.00 35.51 1.82
1739 3978 7.971004 AAAATGAAAACGAGAAGAAACTGTC 57.029 32.000 0.00 0.00 0.00 3.51
1741 3980 6.867662 ATGAAAACGAGAAGAAACTGTCAT 57.132 33.333 0.00 0.00 0.00 3.06
1758 3997 1.135517 TCATCGTTTGATCTCGCGTCA 60.136 47.619 5.77 0.00 30.49 4.35
1764 4003 1.698165 TTGATCTCGCGTCACAACTC 58.302 50.000 5.77 0.00 0.00 3.01
1765 4004 0.596082 TGATCTCGCGTCACAACTCA 59.404 50.000 5.77 0.00 0.00 3.41
1766 4005 0.985549 GATCTCGCGTCACAACTCAC 59.014 55.000 5.77 0.00 0.00 3.51
1767 4006 0.313987 ATCTCGCGTCACAACTCACA 59.686 50.000 5.77 0.00 0.00 3.58
1768 4007 0.101579 TCTCGCGTCACAACTCACAA 59.898 50.000 5.77 0.00 0.00 3.33
1769 4008 0.229753 CTCGCGTCACAACTCACAAC 59.770 55.000 5.77 0.00 0.00 3.32
1770 4009 0.179121 TCGCGTCACAACTCACAACT 60.179 50.000 5.77 0.00 0.00 3.16
1771 4010 1.065851 TCGCGTCACAACTCACAACTA 59.934 47.619 5.77 0.00 0.00 2.24
1772 4011 1.855978 CGCGTCACAACTCACAACTAA 59.144 47.619 0.00 0.00 0.00 2.24
1773 4012 2.475111 CGCGTCACAACTCACAACTAAT 59.525 45.455 0.00 0.00 0.00 1.73
1774 4013 3.671459 CGCGTCACAACTCACAACTAATA 59.329 43.478 0.00 0.00 0.00 0.98
1775 4014 4.326278 CGCGTCACAACTCACAACTAATAT 59.674 41.667 0.00 0.00 0.00 1.28
1776 4015 5.163992 CGCGTCACAACTCACAACTAATATT 60.164 40.000 0.00 0.00 0.00 1.28
1777 4016 6.015504 GCGTCACAACTCACAACTAATATTG 58.984 40.000 0.00 0.00 35.59 1.90
1778 4017 6.015504 CGTCACAACTCACAACTAATATTGC 58.984 40.000 0.00 0.00 32.47 3.56
1779 4018 6.128553 CGTCACAACTCACAACTAATATTGCT 60.129 38.462 0.00 0.00 32.47 3.91
1780 4019 7.062956 CGTCACAACTCACAACTAATATTGCTA 59.937 37.037 0.00 0.00 32.47 3.49
1781 4020 8.383619 GTCACAACTCACAACTAATATTGCTAG 58.616 37.037 0.00 0.00 32.47 3.42
1782 4021 8.311109 TCACAACTCACAACTAATATTGCTAGA 58.689 33.333 0.00 0.00 32.47 2.43
1783 4022 9.102757 CACAACTCACAACTAATATTGCTAGAT 57.897 33.333 0.00 0.00 32.47 1.98
1982 4221 4.101448 ATCTGAGGCGGCGGCTTT 62.101 61.111 36.47 17.02 38.98 3.51
2043 4282 2.053865 CGGTGAGGTAGGCCGGTTA 61.054 63.158 1.90 0.00 41.60 2.85
2056 4295 4.078516 GGTTACCCTCGGCTGCGT 62.079 66.667 0.00 0.00 0.00 5.24
2205 4444 2.616330 CGCTTGCGGATGTTGTGGT 61.616 57.895 7.16 0.00 0.00 4.16
2329 4568 0.389426 GGCGTCGAGGCTAAACTTCA 60.389 55.000 27.24 0.00 42.90 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 18 0.879090 GGGATTTGGTCGGTGTTGTC 59.121 55.000 0.00 0.00 0.00 3.18
17 19 0.887387 CGGGATTTGGTCGGTGTTGT 60.887 55.000 0.00 0.00 0.00 3.32
20 22 2.359478 GCGGGATTTGGTCGGTGT 60.359 61.111 0.00 0.00 0.00 4.16
31 33 1.115326 TCCACATGATCTCGCGGGAT 61.115 55.000 24.12 24.12 0.00 3.85
33 35 1.300465 CTCCACATGATCTCGCGGG 60.300 63.158 6.13 1.01 0.00 6.13
49 51 3.007398 GGGATCATGTGGAGGTATGTCTC 59.993 52.174 0.00 0.00 0.00 3.36
55 57 0.263468 TCGGGGATCATGTGGAGGTA 59.737 55.000 0.00 0.00 0.00 3.08
58 60 1.068083 CGTCGGGGATCATGTGGAG 59.932 63.158 0.00 0.00 0.00 3.86
65 67 2.133281 TCTAACTTCGTCGGGGATCA 57.867 50.000 0.00 0.00 0.00 2.92
68 70 0.529378 GCTTCTAACTTCGTCGGGGA 59.471 55.000 0.00 0.00 0.00 4.81
93 95 3.192944 TCTCAAGTTTGATCCCATCCCT 58.807 45.455 0.00 0.00 36.46 4.20
105 108 8.043710 CCAATAGGAGTAATGTCTCTCAAGTTT 58.956 37.037 0.00 0.00 36.89 2.66
108 111 6.463614 CCCCAATAGGAGTAATGTCTCTCAAG 60.464 46.154 0.00 0.00 38.24 3.02
109 112 5.366768 CCCCAATAGGAGTAATGTCTCTCAA 59.633 44.000 0.00 0.00 38.24 3.02
112 115 5.157770 TCCCCAATAGGAGTAATGTCTCT 57.842 43.478 0.00 0.00 38.24 3.10
128 131 0.742990 GCGACGATGATGTTCCCCAA 60.743 55.000 0.00 0.00 0.00 4.12
131 134 1.153449 TGGCGACGATGATGTTCCC 60.153 57.895 0.00 0.00 0.00 3.97
134 137 0.320334 TGTGTGGCGACGATGATGTT 60.320 50.000 0.00 0.00 0.00 2.71
162 165 4.143389 CGTCTTGTTAGGTTTAGCGTCTTG 60.143 45.833 0.00 0.00 0.00 3.02
209 213 3.132139 CGAAGGACCTCGGCTCGA 61.132 66.667 7.42 0.00 35.14 4.04
212 216 4.070552 GTGCGAAGGACCTCGGCT 62.071 66.667 15.45 0.00 45.47 5.52
225 229 4.738998 TTGGGCCATGGAGGTGCG 62.739 66.667 18.40 0.00 40.61 5.34
227 231 0.967380 GTCTTTGGGCCATGGAGGTG 60.967 60.000 18.40 0.00 40.61 4.00
230 234 0.032813 ATGGTCTTTGGGCCATGGAG 60.033 55.000 18.40 6.39 43.25 3.86
231 235 0.033208 GATGGTCTTTGGGCCATGGA 60.033 55.000 18.40 5.89 44.73 3.41
278 289 0.614979 CTTTCCTCCTCCTCCCGTCA 60.615 60.000 0.00 0.00 0.00 4.35
281 292 2.736826 GCCTTTCCTCCTCCTCCCG 61.737 68.421 0.00 0.00 0.00 5.14
298 309 6.878389 CCTCCTCCATAAGAAAATATCTCAGC 59.122 42.308 0.00 0.00 37.42 4.26
306 317 6.155221 GCCTTTTTCCTCCTCCATAAGAAAAT 59.845 38.462 0.00 0.00 36.59 1.82
314 327 3.201045 GTCTAGCCTTTTTCCTCCTCCAT 59.799 47.826 0.00 0.00 0.00 3.41
316 329 2.572104 TGTCTAGCCTTTTTCCTCCTCC 59.428 50.000 0.00 0.00 0.00 4.30
420 438 6.520272 TCTTTATTTCTAGAGCTGCTCATCC 58.480 40.000 29.49 5.17 32.06 3.51
424 442 6.989169 TCCATTCTTTATTTCTAGAGCTGCTC 59.011 38.462 21.72 21.72 0.00 4.26
452 470 5.539574 TGGTCCAGTCAAACAATCATCATTT 59.460 36.000 0.00 0.00 0.00 2.32
529 549 2.694760 CCTGCAAGCTTTCGGCCTC 61.695 63.158 0.00 0.00 43.05 4.70
608 646 4.143179 CCGTACCACTGTTTCTTCGATTTC 60.143 45.833 0.00 0.00 0.00 2.17
609 647 3.744426 CCGTACCACTGTTTCTTCGATTT 59.256 43.478 0.00 0.00 0.00 2.17
610 648 3.323243 CCGTACCACTGTTTCTTCGATT 58.677 45.455 0.00 0.00 0.00 3.34
611 649 2.353406 CCCGTACCACTGTTTCTTCGAT 60.353 50.000 0.00 0.00 0.00 3.59
880 963 3.204119 CATGCTGGATTCGCCGCA 61.204 61.111 0.00 0.00 45.42 5.69
909 992 1.130054 AGGGAGGCTTCAGTTCAGCA 61.130 55.000 0.00 0.00 39.21 4.41
976 1079 4.077188 GCTTCCGTGTCTGTGCGC 62.077 66.667 0.00 0.00 0.00 6.09
1097 3309 1.532868 GCTGTTGTTGAAGCGTCAGAT 59.467 47.619 1.81 0.00 34.49 2.90
1098 3310 0.937304 GCTGTTGTTGAAGCGTCAGA 59.063 50.000 1.81 0.00 34.49 3.27
1099 3311 0.657312 TGCTGTTGTTGAAGCGTCAG 59.343 50.000 1.81 0.00 42.54 3.51
1100 3312 0.376852 GTGCTGTTGTTGAAGCGTCA 59.623 50.000 0.00 0.00 42.54 4.35
1101 3313 0.657840 AGTGCTGTTGTTGAAGCGTC 59.342 50.000 0.00 0.00 42.54 5.19
1102 3314 0.657840 GAGTGCTGTTGTTGAAGCGT 59.342 50.000 0.00 0.00 42.54 5.07
1103 3315 0.040958 GGAGTGCTGTTGTTGAAGCG 60.041 55.000 0.00 0.00 42.54 4.68
1104 3316 0.312102 GGGAGTGCTGTTGTTGAAGC 59.688 55.000 0.00 0.00 39.96 3.86
1105 3317 1.876156 GAGGGAGTGCTGTTGTTGAAG 59.124 52.381 0.00 0.00 0.00 3.02
1106 3318 1.490490 AGAGGGAGTGCTGTTGTTGAA 59.510 47.619 0.00 0.00 0.00 2.69
1107 3319 1.131638 AGAGGGAGTGCTGTTGTTGA 58.868 50.000 0.00 0.00 0.00 3.18
1108 3320 1.202687 TCAGAGGGAGTGCTGTTGTTG 60.203 52.381 0.00 0.00 33.90 3.33
1109 3321 1.131638 TCAGAGGGAGTGCTGTTGTT 58.868 50.000 0.00 0.00 33.90 2.83
1110 3322 0.394565 GTCAGAGGGAGTGCTGTTGT 59.605 55.000 0.00 0.00 33.90 3.32
1111 3323 0.668706 CGTCAGAGGGAGTGCTGTTG 60.669 60.000 0.00 0.00 33.90 3.33
1112 3324 1.668294 CGTCAGAGGGAGTGCTGTT 59.332 57.895 0.00 0.00 33.90 3.16
1113 3325 2.936912 GCGTCAGAGGGAGTGCTGT 61.937 63.158 0.00 0.00 33.90 4.40
1154 3371 2.279985 CAGCGCTGCTCGATCCAT 60.280 61.111 26.68 0.00 41.67 3.41
1418 3650 4.621068 TCGTTACTTACTCCATGTACGG 57.379 45.455 0.00 0.00 0.00 4.02
1448 3684 5.666969 TTTCATTCCACGACACAAACTAG 57.333 39.130 0.00 0.00 0.00 2.57
1449 3685 5.049060 CCATTTCATTCCACGACACAAACTA 60.049 40.000 0.00 0.00 0.00 2.24
1484 3720 6.375455 CCCTGCTAGTACAAAACTTGATCAAT 59.625 38.462 8.96 0.00 39.80 2.57
1499 3735 1.120530 GGTGCTTAGCCCTGCTAGTA 58.879 55.000 0.29 0.00 42.34 1.82
1500 3736 1.908483 GGTGCTTAGCCCTGCTAGT 59.092 57.895 0.29 0.00 42.34 2.57
1501 3737 1.227380 CGGTGCTTAGCCCTGCTAG 60.227 63.158 0.29 0.00 42.34 3.42
1533 3769 9.838339 TCTCAGTTCTTTCTTTCTTTCTAATGT 57.162 29.630 0.00 0.00 0.00 2.71
1542 3778 7.607991 TCTGTGTTTTCTCAGTTCTTTCTTTCT 59.392 33.333 0.00 0.00 40.82 2.52
1549 3785 4.775236 AGCTCTGTGTTTTCTCAGTTCTT 58.225 39.130 0.00 0.00 40.82 2.52
1550 3786 4.414337 AGCTCTGTGTTTTCTCAGTTCT 57.586 40.909 0.00 0.00 40.82 3.01
1551 3787 4.151512 GCTAGCTCTGTGTTTTCTCAGTTC 59.848 45.833 7.70 0.00 40.82 3.01
1569 3805 1.813178 GGGTCCAAAAACTGAGCTAGC 59.187 52.381 6.62 6.62 0.00 3.42
1591 3827 1.121240 CGACGTTCGCCAGCTATTAG 58.879 55.000 0.00 0.00 31.14 1.73
1592 3828 3.245443 CGACGTTCGCCAGCTATTA 57.755 52.632 0.00 0.00 31.14 0.98
1593 3829 4.088421 CGACGTTCGCCAGCTATT 57.912 55.556 0.00 0.00 31.14 1.73
1608 3844 0.179121 AATGTTATCCGTCGCAGCGA 60.179 50.000 15.11 15.11 0.00 4.93
1609 3845 0.650512 AAATGTTATCCGTCGCAGCG 59.349 50.000 9.06 9.06 0.00 5.18
1614 3853 2.092995 TGTTCGCAAATGTTATCCGTCG 59.907 45.455 0.00 0.00 0.00 5.12
1617 3856 5.004345 GGAAAATGTTCGCAAATGTTATCCG 59.996 40.000 0.00 0.00 34.28 4.18
1622 3861 4.511082 CCAAGGAAAATGTTCGCAAATGTT 59.489 37.500 0.00 0.00 34.28 2.71
1635 3874 5.327732 TCTGAAGAATCTGCCAAGGAAAAT 58.672 37.500 0.00 0.00 0.00 1.82
1640 3879 3.269178 GTCTCTGAAGAATCTGCCAAGG 58.731 50.000 0.00 0.00 31.93 3.61
1661 3900 5.105063 TGTCTCTGAAGAAGATGTTATGCG 58.895 41.667 0.00 0.00 33.29 4.73
1666 3905 6.994496 TGTCATTTGTCTCTGAAGAAGATGTT 59.006 34.615 0.00 0.00 33.29 2.71
1667 3906 6.528321 TGTCATTTGTCTCTGAAGAAGATGT 58.472 36.000 0.00 0.00 33.29 3.06
1671 3910 6.857777 AACTGTCATTTGTCTCTGAAGAAG 57.142 37.500 0.00 0.00 31.93 2.85
1685 3924 8.477419 TTTTATTCTTCCCAGAAACTGTCATT 57.523 30.769 0.00 0.00 42.53 2.57
1714 3953 8.670135 TGACAGTTTCTTCTCGTTTTCATTTTA 58.330 29.630 0.00 0.00 0.00 1.52
1716 3955 7.083875 TGACAGTTTCTTCTCGTTTTCATTT 57.916 32.000 0.00 0.00 0.00 2.32
1717 3956 6.677781 TGACAGTTTCTTCTCGTTTTCATT 57.322 33.333 0.00 0.00 0.00 2.57
1718 3957 6.346919 CGATGACAGTTTCTTCTCGTTTTCAT 60.347 38.462 0.00 0.00 0.00 2.57
1719 3958 5.051039 CGATGACAGTTTCTTCTCGTTTTCA 60.051 40.000 0.00 0.00 0.00 2.69
1720 3959 5.050972 ACGATGACAGTTTCTTCTCGTTTTC 60.051 40.000 0.00 0.00 33.58 2.29
1729 3968 5.119279 CGAGATCAAACGATGACAGTTTCTT 59.881 40.000 0.00 0.00 41.93 2.52
1730 3969 4.623167 CGAGATCAAACGATGACAGTTTCT 59.377 41.667 0.00 0.00 41.93 2.52
1739 3978 1.007011 GTGACGCGAGATCAAACGATG 60.007 52.381 15.93 4.05 0.00 3.84
1741 3980 0.039888 TGTGACGCGAGATCAAACGA 60.040 50.000 15.93 0.00 0.00 3.85
1778 4017 7.429633 CGGATCTGGGTTATTGCTATATCTAG 58.570 42.308 0.00 0.00 0.00 2.43
1779 4018 6.323996 CCGGATCTGGGTTATTGCTATATCTA 59.676 42.308 13.34 0.00 0.00 1.98
1780 4019 5.129485 CCGGATCTGGGTTATTGCTATATCT 59.871 44.000 13.34 0.00 0.00 1.98
1781 4020 5.360591 CCGGATCTGGGTTATTGCTATATC 58.639 45.833 13.34 0.00 0.00 1.63
1782 4021 4.384208 GCCGGATCTGGGTTATTGCTATAT 60.384 45.833 22.38 0.00 0.00 0.86
1783 4022 3.055385 GCCGGATCTGGGTTATTGCTATA 60.055 47.826 22.38 0.00 0.00 1.31
1784 4023 2.290323 GCCGGATCTGGGTTATTGCTAT 60.290 50.000 22.38 0.00 0.00 2.97
1785 4024 1.071699 GCCGGATCTGGGTTATTGCTA 59.928 52.381 22.38 0.00 0.00 3.49
1786 4025 0.179018 GCCGGATCTGGGTTATTGCT 60.179 55.000 22.38 0.00 0.00 3.91
1787 4026 1.507141 CGCCGGATCTGGGTTATTGC 61.507 60.000 22.38 4.73 0.00 3.56
1788 4027 0.884704 CCGCCGGATCTGGGTTATTG 60.885 60.000 22.38 0.00 0.00 1.90
1789 4028 1.450211 CCGCCGGATCTGGGTTATT 59.550 57.895 22.38 0.00 0.00 1.40
1790 4029 3.148084 CCGCCGGATCTGGGTTAT 58.852 61.111 22.38 0.00 0.00 1.89
1791 4030 3.857038 GCCGCCGGATCTGGGTTA 61.857 66.667 22.38 0.00 0.00 2.85
2205 4444 4.323477 CCGCCACCTCCGAACCAA 62.323 66.667 0.00 0.00 0.00 3.67
2235 4474 2.116556 GCCAAAGGTTTCCCCCGA 59.883 61.111 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.