Multiple sequence alignment - TraesCS2B01G375800

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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 TraesCS2B01G375800 chr2B 100.000 4040 0 0 1 4040 538951455 538955494 0.000000e+00 7461.0
1 TraesCS2B01G375800 chr2D 90.980 3836 173 62 1 3733 457650447 457654212 0.000000e+00 5007.0
2 TraesCS2B01G375800 chr2D 87.547 265 19 6 3778 4040 457654409 457654661 1.100000e-75 294.0
3 TraesCS2B01G375800 chr2D 93.617 47 3 0 2210 2256 75504933 75504979 2.010000e-08 71.3
4 TraesCS2B01G375800 chr2A 89.846 1822 109 35 2253 4040 601336567 601338346 0.000000e+00 2270.0
5 TraesCS2B01G375800 chr2A 90.448 1497 87 14 727 2191 601335098 601336570 0.000000e+00 1921.0
6 TraesCS2B01G375800 chr2A 88.591 298 25 8 48 338 601334268 601334563 1.790000e-93 353.0
7 TraesCS2B01G375800 chr7A 96.774 93 1 1 3815 3907 209593022 209592932 1.940000e-33 154.0
8 TraesCS2B01G375800 chr7A 100.000 35 0 0 2216 2250 60725627 60725593 9.370000e-07 65.8
9 TraesCS2B01G375800 chr7D 94.737 95 3 1 3812 3906 199564319 199564227 3.250000e-31 147.0
10 TraesCS2B01G375800 chr7D 89.130 46 3 2 325 369 554577928 554577884 5.640000e-04 56.5
11 TraesCS2B01G375800 chr3B 93.939 99 3 3 3816 3913 805612445 805612349 3.250000e-31 147.0
12 TraesCS2B01G375800 chr3B 93.939 99 3 3 3816 3913 805619234 805619138 3.250000e-31 147.0
13 TraesCS2B01G375800 chr3B 93.617 94 3 2 3816 3907 822106194 822106286 1.960000e-28 137.0
14 TraesCS2B01G375800 chr3B 91.304 46 3 1 2209 2254 161638137 161638093 1.210000e-05 62.1
15 TraesCS2B01G375800 chr3D 93.617 94 5 1 3817 3909 610081372 610081465 5.440000e-29 139.0
16 TraesCS2B01G375800 chr3D 93.617 94 4 2 3808 3899 610184414 610184507 5.440000e-29 139.0
17 TraesCS2B01G375800 chr1A 93.617 47 3 0 2209 2255 495704692 495704738 2.010000e-08 71.3
18 TraesCS2B01G375800 chr1A 91.667 48 4 0 2210 2257 148958930 148958977 2.610000e-07 67.6


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 TraesCS2B01G375800 chr2B 538951455 538955494 4039 False 7461.000000 7461 100.000000 1 4040 1 chr2B.!!$F1 4039
1 TraesCS2B01G375800 chr2D 457650447 457654661 4214 False 2650.500000 5007 89.263500 1 4040 2 chr2D.!!$F2 4039
2 TraesCS2B01G375800 chr2A 601334268 601338346 4078 False 1514.666667 2270 89.628333 48 4040 3 chr2A.!!$F1 3992

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 0.036022 AGAGTGGAAGCCTCAGTTGC 59.964 55.0 0.00 0.00 0.0 4.17 F
86 87 0.250124 TGCGATCCGTGGTTTGTTCT 60.250 50.0 0.00 0.00 0.0 3.01 F
1354 1570 0.245266 TTGCTTATGAGTGTCGGCGA 59.755 50.0 4.99 4.99 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1452 0.031994 GCGAGATCTGAAGAGAGGGC 59.968 60.000 0.00 0.00 0.00 5.19 R
1634 1857 1.608283 GCAGGTGGAACTGTCTGGTAC 60.608 57.143 0.00 0.00 40.59 3.34 R
3120 3393 1.195900 CAAACATTACACGTGGACCCG 59.804 52.381 21.57 4.53 0.00 5.28 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
65 66 2.738000 CGAATCAGAGTGGAAGCCTCAG 60.738 54.545 0.00 0.00 0.00 3.35
69 70 0.036022 AGAGTGGAAGCCTCAGTTGC 59.964 55.000 0.00 0.00 0.00 4.17
86 87 0.250124 TGCGATCCGTGGTTTGTTCT 60.250 50.000 0.00 0.00 0.00 3.01
93 94 1.953686 CCGTGGTTTGTTCTGTCCATT 59.046 47.619 0.00 0.00 32.45 3.16
111 112 2.857380 TTTGTTGTGTGCGTGCGTGG 62.857 55.000 0.00 0.00 0.00 4.94
113 114 3.128188 TTGTGTGCGTGCGTGGTT 61.128 55.556 0.00 0.00 0.00 3.67
170 176 1.376812 GGTCGGCCAAACTGGGTAG 60.377 63.158 0.00 0.00 38.19 3.18
200 207 6.034150 TGTTATGTTATCAACGTCGTGATGAC 59.966 38.462 14.85 14.85 42.14 3.06
229 236 0.527565 ACCTGCGTTCCATTTCATGC 59.472 50.000 0.00 0.00 0.00 4.06
260 268 3.941483 GCACCACTGCAGACTAATAATGT 59.059 43.478 23.35 0.65 43.62 2.71
340 348 1.866853 GCCAGGGCTTCTTTGGTTCG 61.867 60.000 2.30 0.00 38.26 3.95
346 354 2.227194 GGCTTCTTTGGTTCGAAGGAA 58.773 47.619 0.00 0.00 37.65 3.36
379 459 4.953940 TTTGGAAGGATTTGAACCCTTG 57.046 40.909 0.00 0.00 42.43 3.61
405 486 6.657541 GGAATTTGTCCTGTGATGGTAGTTTA 59.342 38.462 0.00 0.00 43.98 2.01
423 504 7.973944 GGTAGTTTAATTCGCAGGATTGAAATT 59.026 33.333 0.00 0.00 0.00 1.82
424 505 7.816945 AGTTTAATTCGCAGGATTGAAATTG 57.183 32.000 0.00 0.00 0.00 2.32
459 540 4.771114 TCCATAGGGTCCATTTGTACTG 57.229 45.455 0.00 0.00 34.93 2.74
467 548 4.021544 GGGTCCATTTGTACTGCATTTTGA 60.022 41.667 0.00 0.00 0.00 2.69
475 556 8.776470 CATTTGTACTGCATTTTGAAGGAAAAT 58.224 29.630 0.00 0.00 43.77 1.82
493 574 7.670364 AGGAAAATTTTCATCCACCTACTTTG 58.330 34.615 27.53 0.00 38.92 2.77
501 582 1.156736 CCACCTACTTTGTTCCTGCG 58.843 55.000 0.00 0.00 0.00 5.18
536 693 4.918810 ATTCCTGCGTTTTGATAATCCC 57.081 40.909 0.00 0.00 0.00 3.85
537 694 2.285083 TCCTGCGTTTTGATAATCCCG 58.715 47.619 0.00 0.00 0.00 5.14
596 754 1.471684 AGTTGAGATACACCGACCGTC 59.528 52.381 0.00 0.00 0.00 4.79
630 788 3.435186 GAAGCTGGCTTGCGACCC 61.435 66.667 12.79 0.00 36.26 4.46
640 798 1.219522 CTTGCGACCCGACGTTTTCT 61.220 55.000 0.00 0.00 35.59 2.52
675 833 4.648626 TCGGGTCCGTCTCCACGT 62.649 66.667 9.36 0.00 45.17 4.49
725 896 2.780643 CAATCCAGTGCACGAGCG 59.219 61.111 12.01 1.29 46.23 5.03
878 1079 2.202878 CACCACCATCGCCCTACG 60.203 66.667 0.00 0.00 45.62 3.51
881 1082 4.910585 CACCATCGCCCTACGCCC 62.911 72.222 0.00 0.00 43.23 6.13
919 1120 1.082104 GAGAAAACCACCGCAAGCG 60.082 57.895 7.60 7.60 39.44 4.68
966 1171 3.665675 GAATCCGGCAGGCACGAGT 62.666 63.158 0.00 0.00 37.47 4.18
1281 1497 3.240069 ACGCGCGATTATCTACATAACC 58.760 45.455 39.36 0.00 0.00 2.85
1286 1502 5.844396 GCGCGATTATCTACATAACCAAAAC 59.156 40.000 12.10 0.00 0.00 2.43
1304 1520 4.452733 GGGCCCGTCGGTTGAGAG 62.453 72.222 5.69 0.00 0.00 3.20
1305 1521 3.692406 GGCCCGTCGGTTGAGAGT 61.692 66.667 11.06 0.00 0.00 3.24
1306 1522 2.342648 GCCCGTCGGTTGAGAGTT 59.657 61.111 11.06 0.00 0.00 3.01
1307 1523 2.027625 GCCCGTCGGTTGAGAGTTG 61.028 63.158 11.06 0.00 0.00 3.16
1308 1524 1.663739 CCCGTCGGTTGAGAGTTGA 59.336 57.895 11.06 0.00 0.00 3.18
1309 1525 0.388649 CCCGTCGGTTGAGAGTTGAG 60.389 60.000 11.06 0.00 0.00 3.02
1310 1526 0.596577 CCGTCGGTTGAGAGTTGAGA 59.403 55.000 2.08 0.00 0.00 3.27
1315 1531 3.502979 GTCGGTTGAGAGTTGAGACTAGT 59.497 47.826 0.00 0.00 35.88 2.57
1354 1570 0.245266 TTGCTTATGAGTGTCGGCGA 59.755 50.000 4.99 4.99 0.00 5.54
1362 1578 1.270094 TGAGTGTCGGCGAACTGAATT 60.270 47.619 22.80 5.42 31.36 2.17
1364 1580 1.000955 AGTGTCGGCGAACTGAATTCT 59.999 47.619 12.92 0.00 34.88 2.40
1367 1583 2.288825 TGTCGGCGAACTGAATTCTCTT 60.289 45.455 12.92 0.00 34.88 2.85
1380 1596 7.199766 ACTGAATTCTCTTCTAGCAATAGACG 58.800 38.462 7.05 0.00 0.00 4.18
1386 1602 9.685828 ATTCTCTTCTAGCAATAGACGATTTAC 57.314 33.333 0.00 0.00 0.00 2.01
1388 1604 8.346300 TCTCTTCTAGCAATAGACGATTTACTG 58.654 37.037 0.00 0.00 0.00 2.74
1417 1639 5.410439 TGCTTTTAACTGGGTCGATAAACTC 59.590 40.000 0.00 0.00 0.00 3.01
1428 1650 4.563184 GGTCGATAAACTCATGTCTGACAC 59.437 45.833 13.50 0.00 0.00 3.67
1435 1657 4.330944 ACTCATGTCTGACACGGTTTTA 57.669 40.909 13.50 0.00 0.00 1.52
1539 1762 9.255304 GTTCAGTATTATCCAGTCTTCTCATTC 57.745 37.037 0.00 0.00 0.00 2.67
1626 1849 5.698089 TCACTTGTGAAGTTCTGATCATGAC 59.302 40.000 0.00 0.00 40.46 3.06
1634 1857 7.749570 GTGAAGTTCTGATCATGACATTTTCTG 59.250 37.037 0.00 0.00 0.00 3.02
1687 1911 8.118600 AGATTTTTCTGGAATCTTATCACCCTT 58.881 33.333 0.00 0.00 40.07 3.95
1696 1920 4.188247 TCTTATCACCCTTCGACACAAG 57.812 45.455 0.00 0.00 0.00 3.16
1717 1941 3.197116 AGTTAGACGTCCAGGGTTATTGG 59.803 47.826 13.01 0.00 37.04 3.16
1790 2016 3.311322 TGTTTGAAAAGTAGTGCCTGTCG 59.689 43.478 0.00 0.00 0.00 4.35
1809 2035 4.688879 TGTCGGCAGTACTGAAGTTTTATG 59.311 41.667 27.08 4.53 34.69 1.90
1810 2036 4.689345 GTCGGCAGTACTGAAGTTTTATGT 59.311 41.667 27.08 0.00 34.69 2.29
1930 2156 1.356124 AGTATCAGGCTGGCCATAGG 58.644 55.000 15.73 0.00 38.92 2.57
1943 2169 2.159198 GGCCATAGGTCATTTTGCAGTG 60.159 50.000 0.00 0.00 0.00 3.66
2202 2461 8.404765 GGTCTAACTATTACTACCTCTGTTCAC 58.595 40.741 0.00 0.00 0.00 3.18
2226 2485 8.487176 CACTAATGTAAATTGAACTGCCAAAAC 58.513 33.333 0.00 0.00 0.00 2.43
2278 2537 6.835488 ACTTCTTATGTGCAATACCATCCAAT 59.165 34.615 0.00 0.00 0.00 3.16
2336 2595 5.417580 GCAACCAAACATGGATTACTTCCTA 59.582 40.000 1.10 0.00 45.68 2.94
2424 2686 3.010420 GTGATTACTCCCCTGCACTTTC 58.990 50.000 0.00 0.00 0.00 2.62
2450 2712 0.179020 TGTGCTGCTTACCAAGTGCT 60.179 50.000 0.00 0.00 33.52 4.40
2493 2755 6.699366 TGTCGGTAGTTATTTATCAACCACA 58.301 36.000 0.00 0.00 0.00 4.17
2525 2791 1.246649 CACCTGCACACATGGCTTTA 58.753 50.000 0.00 0.00 0.00 1.85
2542 2808 6.354130 TGGCTTTAACCTACATAACTCATCC 58.646 40.000 0.00 0.00 0.00 3.51
2652 2918 8.940952 TGGAACTTTTGTTGTAAATTCCTTTTG 58.059 29.630 0.00 0.00 43.66 2.44
2971 3238 4.594920 TCTCAAAGGAGAGGAAACTGACAT 59.405 41.667 0.00 0.00 45.12 3.06
3120 3393 2.348666 CACCGAGCAATGTTAGCTGTAC 59.651 50.000 0.00 0.00 43.58 2.90
3252 3530 9.910511 AAATATGAAGCTTTATTGTAACGTACG 57.089 29.630 15.01 15.01 0.00 3.67
3294 3572 3.325293 AGTGTTGTGGCTGTAGATCAG 57.675 47.619 0.00 0.00 46.12 2.90
3317 3595 2.380410 CGGTTTCTGCCTTCGACGG 61.380 63.158 3.00 3.00 0.00 4.79
3358 3636 5.868043 TCTGCAGTTTGATTCACAGTATG 57.132 39.130 14.67 0.00 46.00 2.39
3471 3780 1.337447 GCTAGTGCTTGGTACCGTCAA 60.337 52.381 7.57 0.00 36.03 3.18
3488 3797 3.637432 GTCAAATGTTCGGAATGTGCAA 58.363 40.909 0.00 0.00 0.00 4.08
3544 3856 1.827399 TTGAAGGGCGGAGACACCTC 61.827 60.000 0.00 0.00 37.00 3.85
3580 3892 3.820467 TCAGTGCTTGTAGTTGGGAAATG 59.180 43.478 0.00 0.00 0.00 2.32
3740 4076 6.076981 CCAGCAGGTTCATGGAAATAATAC 57.923 41.667 0.00 0.00 36.09 1.89
3743 4079 5.300286 AGCAGGTTCATGGAAATAATACTGC 59.700 40.000 0.00 0.00 45.63 4.40
3744 4080 5.067674 GCAGGTTCATGGAAATAATACTGCA 59.932 40.000 0.00 0.00 44.90 4.41
3745 4081 6.498304 CAGGTTCATGGAAATAATACTGCAC 58.502 40.000 0.00 0.00 0.00 4.57
3746 4082 5.594317 AGGTTCATGGAAATAATACTGCACC 59.406 40.000 0.00 0.00 0.00 5.01
3747 4083 5.594317 GGTTCATGGAAATAATACTGCACCT 59.406 40.000 0.00 0.00 0.00 4.00
3814 4305 4.994756 AGGCCGGTGCAAAAGGGG 62.995 66.667 1.90 0.00 40.13 4.79
3857 4348 1.340248 GTCTCGAACCTGTGACCTTCA 59.660 52.381 0.00 0.00 0.00 3.02
3909 4400 7.627939 GCTGAGCTAATAGGCCAATTTGATATG 60.628 40.741 5.01 0.00 0.00 1.78
3910 4401 7.460910 TGAGCTAATAGGCCAATTTGATATGA 58.539 34.615 5.01 0.00 0.00 2.15
3967 4458 8.934023 TTAAGAGAACCAAGGAAAACACATAT 57.066 30.769 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 0.309612 AACAAACCACGGATCGCAAC 59.690 50.000 0.00 0.00 0.00 4.17
69 70 1.459592 GACAGAACAAACCACGGATCG 59.540 52.381 0.00 0.00 0.00 3.69
86 87 1.098869 ACGCACACAACAAATGGACA 58.901 45.000 0.00 0.00 0.00 4.02
93 94 2.099254 CACGCACGCACACAACAA 59.901 55.556 0.00 0.00 0.00 2.83
153 159 2.038837 GCTACCCAGTTTGGCCGAC 61.039 63.158 0.00 0.00 35.79 4.79
170 176 4.955590 CGACGTTGATAACATAACATGTGC 59.044 41.667 0.00 0.00 44.07 4.57
260 268 1.253100 TAGTGGTGATGCACGACAGA 58.747 50.000 13.69 0.70 43.68 3.41
340 348 8.200120 CCTTCCAAAATCCTATGAAATTCCTTC 58.800 37.037 0.00 0.00 34.31 3.46
346 354 9.270707 TCAAATCCTTCCAAAATCCTATGAAAT 57.729 29.630 0.00 0.00 0.00 2.17
405 486 6.152661 TCCTAACAATTTCAATCCTGCGAATT 59.847 34.615 0.00 0.00 0.00 2.17
439 520 3.214328 GCAGTACAAATGGACCCTATGG 58.786 50.000 0.00 0.00 37.80 2.74
459 540 7.804600 GTGGATGAAAATTTTCCTTCAAAATGC 59.195 33.333 24.51 15.80 42.86 3.56
467 548 7.855784 AAGTAGGTGGATGAAAATTTTCCTT 57.144 32.000 24.51 14.15 36.36 3.36
475 556 5.534654 CAGGAACAAAGTAGGTGGATGAAAA 59.465 40.000 0.00 0.00 0.00 2.29
512 669 5.763204 GGGATTATCAAAACGCAGGAATAGA 59.237 40.000 0.00 0.00 0.00 1.98
536 693 1.856597 CCTCTTTAATCCGTAACCGCG 59.143 52.381 0.00 0.00 0.00 6.46
537 694 1.596260 GCCTCTTTAATCCGTAACCGC 59.404 52.381 0.00 0.00 0.00 5.68
596 754 1.837538 TTCGTTTCTTTCGCCCGCAG 61.838 55.000 0.00 0.00 0.00 5.18
630 788 0.782384 CAAGTCCGGAGAAAACGTCG 59.218 55.000 3.06 0.00 0.00 5.12
640 798 2.550606 CCGAAATTTTGACAAGTCCGGA 59.449 45.455 0.00 0.00 36.86 5.14
741 937 2.034221 GTGGGCAGTGAAGGTCCC 59.966 66.667 0.00 0.00 39.22 4.46
862 1063 4.157120 GCGTAGGGCGATGGTGGT 62.157 66.667 0.00 0.00 44.77 4.16
881 1082 3.297620 GTTGCTGTGGCCTGTGGG 61.298 66.667 3.32 0.00 37.74 4.61
882 1083 2.519063 TGTTGCTGTGGCCTGTGG 60.519 61.111 3.32 0.00 37.74 4.17
884 1085 2.901840 CGTGTTGCTGTGGCCTGT 60.902 61.111 3.32 0.00 37.74 4.00
886 1087 2.281070 CTCGTGTTGCTGTGGCCT 60.281 61.111 3.32 0.00 37.74 5.19
887 1088 1.444119 TTTCTCGTGTTGCTGTGGCC 61.444 55.000 0.00 0.00 37.74 5.36
888 1089 0.380378 TTTTCTCGTGTTGCTGTGGC 59.620 50.000 0.00 0.00 39.26 5.01
947 1152 3.376935 CTCGTGCCTGCCGGATTCT 62.377 63.158 5.05 0.00 0.00 2.40
1194 1410 1.112315 CGATGGACTGGAGGGAGAGG 61.112 65.000 0.00 0.00 0.00 3.69
1229 1445 3.787001 GAAGAGAGGGCGGGGGTG 61.787 72.222 0.00 0.00 0.00 4.61
1230 1446 4.332543 TGAAGAGAGGGCGGGGGT 62.333 66.667 0.00 0.00 0.00 4.95
1233 1449 0.758685 AGATCTGAAGAGAGGGCGGG 60.759 60.000 0.00 0.00 0.00 6.13
1236 1452 0.031994 GCGAGATCTGAAGAGAGGGC 59.968 60.000 0.00 0.00 0.00 5.19
1270 1486 3.284617 GGCCCGTTTTGGTTATGTAGAT 58.715 45.455 0.00 0.00 35.15 1.98
1315 1531 1.903860 ACCGCATCCACCTAGTTAACA 59.096 47.619 8.61 0.00 0.00 2.41
1354 1570 7.704472 CGTCTATTGCTAGAAGAGAATTCAGTT 59.296 37.037 8.44 0.00 36.04 3.16
1362 1578 8.346300 CAGTAAATCGTCTATTGCTAGAAGAGA 58.654 37.037 0.00 0.00 42.96 3.10
1364 1580 7.997482 ACAGTAAATCGTCTATTGCTAGAAGA 58.003 34.615 0.00 2.04 43.56 2.87
1386 1602 6.046593 TCGACCCAGTTAAAAGCATATACAG 58.953 40.000 0.00 0.00 0.00 2.74
1388 1604 8.597662 TTATCGACCCAGTTAAAAGCATATAC 57.402 34.615 0.00 0.00 0.00 1.47
1406 1628 4.263209 CGTGTCAGACATGAGTTTATCGAC 59.737 45.833 16.81 0.00 37.29 4.20
1417 1639 5.356882 AATGTAAAACCGTGTCAGACATG 57.643 39.130 15.07 15.07 34.96 3.21
1428 1650 4.684242 GCAAAGGAAGGAAATGTAAAACCG 59.316 41.667 0.00 0.00 0.00 4.44
1435 1657 2.250924 CCCTGCAAAGGAAGGAAATGT 58.749 47.619 0.00 0.00 43.45 2.71
1634 1857 1.608283 GCAGGTGGAACTGTCTGGTAC 60.608 57.143 0.00 0.00 40.59 3.34
1687 1911 1.948834 TGGACGTCTAACTTGTGTCGA 59.051 47.619 16.46 0.00 0.00 4.20
1696 1920 3.528532 CCAATAACCCTGGACGTCTAAC 58.471 50.000 16.46 0.00 35.85 2.34
1717 1941 3.866910 CACCATTAAAATGACAGGCATGC 59.133 43.478 9.90 9.90 38.70 4.06
1790 2016 7.040961 TGGTTAACATAAAACTTCAGTACTGCC 60.041 37.037 18.45 7.89 0.00 4.85
1858 2084 4.946478 TGAACATAAAACAAACTGGGGG 57.054 40.909 0.00 0.00 0.00 5.40
1891 2117 7.972277 TGATACTTAACTCGCCAGTAGTTTAAG 59.028 37.037 0.00 0.00 38.18 1.85
1930 2156 4.972440 GTCTTTCAGACACTGCAAAATGAC 59.028 41.667 0.00 0.00 44.45 3.06
1943 2169 5.244178 TCCTTAAGAGTCAGGTCTTTCAGAC 59.756 44.000 3.36 0.00 44.32 3.51
1954 2180 6.634805 TCATGCTAAAGTCCTTAAGAGTCAG 58.365 40.000 3.36 0.00 0.00 3.51
1955 2181 6.605471 TCATGCTAAAGTCCTTAAGAGTCA 57.395 37.500 3.36 0.00 0.00 3.41
1956 2182 7.148390 GGTTTCATGCTAAAGTCCTTAAGAGTC 60.148 40.741 3.36 0.00 0.00 3.36
1957 2183 6.655425 GGTTTCATGCTAAAGTCCTTAAGAGT 59.345 38.462 3.36 0.00 0.00 3.24
1958 2184 6.881602 AGGTTTCATGCTAAAGTCCTTAAGAG 59.118 38.462 3.36 0.00 0.00 2.85
1959 2185 6.655003 CAGGTTTCATGCTAAAGTCCTTAAGA 59.345 38.462 3.36 0.00 0.00 2.10
1960 2186 6.431234 ACAGGTTTCATGCTAAAGTCCTTAAG 59.569 38.462 0.00 0.00 0.00 1.85
2011 2244 9.764363 TTAGCAAATATACACTAGGTCATTCAG 57.236 33.333 0.00 0.00 0.00 3.02
2202 2461 8.816640 AGTTTTGGCAGTTCAATTTACATTAG 57.183 30.769 0.00 0.00 0.00 1.73
2226 2485 9.892130 ACAACCTCTGTTCCTAAATATAAGAAG 57.108 33.333 0.00 0.00 32.99 2.85
2249 2508 7.282224 GGATGGTATTGCACATAAGAAGTACAA 59.718 37.037 0.00 0.00 0.00 2.41
2298 2557 8.607459 CATGTTTGGTTGCAAAAAGTTAATGTA 58.393 29.630 0.00 0.00 0.00 2.29
2336 2595 8.807948 AATGTTAATGTGCTACTGGAAATAGT 57.192 30.769 0.00 0.00 34.71 2.12
2436 2698 2.340210 TTGTCAGCACTTGGTAAGCA 57.660 45.000 0.00 0.00 0.00 3.91
2493 2755 1.318576 GCAGGTGTGGTGCTAGTTTT 58.681 50.000 0.00 0.00 37.96 2.43
2525 2791 6.540438 TCGAAAGGATGAGTTATGTAGGTT 57.460 37.500 0.00 0.00 0.00 3.50
2542 2808 8.673626 AGCATTTGTAATTGTACAATCGAAAG 57.326 30.769 21.02 12.97 46.91 2.62
2595 2861 1.325355 CTTGGGCAGCAATATGGGAG 58.675 55.000 0.00 0.00 0.00 4.30
2652 2918 4.036027 CCTCATAACAGATGCAACCATGTC 59.964 45.833 0.00 0.00 0.00 3.06
2704 2971 1.862815 GCCGCAAGCTGCATATTTCAG 60.863 52.381 1.02 0.00 45.36 3.02
2971 3238 1.658114 CTCGACGTTCCCACAGTGA 59.342 57.895 0.62 0.00 0.00 3.41
3071 3338 2.967599 ATGTCGTCTGCTGCAGATAA 57.032 45.000 32.45 21.24 42.73 1.75
3075 3342 2.693797 AAAAATGTCGTCTGCTGCAG 57.306 45.000 23.31 23.31 0.00 4.41
3120 3393 1.195900 CAAACATTACACGTGGACCCG 59.804 52.381 21.57 4.53 0.00 5.28
3249 3527 9.946165 CTACACTGAATGTCTTCAATATACGTA 57.054 33.333 0.00 0.00 42.09 3.57
3250 3528 8.467598 ACTACACTGAATGTCTTCAATATACGT 58.532 33.333 0.00 0.00 42.09 3.57
3251 3529 8.746751 CACTACACTGAATGTCTTCAATATACG 58.253 37.037 0.00 0.00 42.09 3.06
3252 3530 9.587772 ACACTACACTGAATGTCTTCAATATAC 57.412 33.333 0.00 0.00 42.09 1.47
3317 3595 5.032863 GCAGATGTGTGCATTACTGAATTC 58.967 41.667 0.00 0.00 43.41 2.17
3383 3668 0.323816 AGATCTGTCTCCACGAGCCA 60.324 55.000 0.00 0.00 0.00 4.75
3467 3776 3.281341 TGCACATTCCGAACATTTGAC 57.719 42.857 0.00 0.00 0.00 3.18
3471 3780 6.753279 CAGAAATATTGCACATTCCGAACATT 59.247 34.615 0.00 0.00 0.00 2.71
3488 3797 6.058183 GGTGTCTCCATGCTAACAGAAATAT 58.942 40.000 0.00 0.00 35.97 1.28
3544 3856 5.523916 ACAAGCACTGAACAGTACTAACTTG 59.476 40.000 19.55 19.55 40.20 3.16
3670 4006 4.351111 GGGATGGAGGGAGTATTACATGTT 59.649 45.833 2.30 0.00 0.00 2.71
3672 4008 3.909995 TGGGATGGAGGGAGTATTACATG 59.090 47.826 0.00 0.00 0.00 3.21
3746 4082 5.120830 GTGCAGTATTGTTTCCTGAGTACAG 59.879 44.000 0.00 0.00 43.12 2.74
3747 4083 4.994852 GTGCAGTATTGTTTCCTGAGTACA 59.005 41.667 0.00 0.00 0.00 2.90
3760 4207 5.643348 TGACATTTCTACAGGTGCAGTATTG 59.357 40.000 0.00 0.00 0.00 1.90
3764 4211 3.071602 ACTGACATTTCTACAGGTGCAGT 59.928 43.478 0.00 0.00 36.17 4.40
3799 4290 2.034048 TTTTCCCCTTTTGCACCGGC 62.034 55.000 0.00 0.00 41.68 6.13
3936 4427 9.416284 TGTTTTCCTTGGTTCTCTTAAGTTATT 57.584 29.630 1.63 0.00 0.00 1.40
3937 4428 8.847196 GTGTTTTCCTTGGTTCTCTTAAGTTAT 58.153 33.333 1.63 0.00 0.00 1.89
3945 4436 7.393515 GGTAATATGTGTTTTCCTTGGTTCTCT 59.606 37.037 0.00 0.00 0.00 3.10
3967 4458 0.834612 ATCTGATTTCGGGGCGGTAA 59.165 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.