Multiple sequence alignment - TraesCS4D01G134000

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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 TraesCS4D01G134000 chr4D 100.000 4880 0 0 1 4880 120886264 120881385 0.000000e+00 9012.0
1 TraesCS4D01G134000 chr4D 83.565 432 50 14 1474 1901 327379506 327379920 7.660000e-103 385.0
2 TraesCS4D01G134000 chr4D 88.800 125 14 0 1 125 121074083 121073959 2.350000e-33 154.0
3 TraesCS4D01G134000 chr4A 95.011 2846 84 28 229 3042 452350369 452347550 0.000000e+00 4416.0
4 TraesCS4D01G134000 chr4A 92.417 1411 83 14 2737 4138 452347553 452346158 0.000000e+00 1991.0
5 TraesCS4D01G134000 chr4A 95.211 710 33 1 4172 4880 143443867 143443158 0.000000e+00 1122.0
6 TraesCS4D01G134000 chr4A 96.507 229 8 0 1 229 452359088 452358860 3.560000e-101 379.0
7 TraesCS4D01G134000 chr4A 79.630 432 57 16 1474 1901 143701511 143701107 1.030000e-71 281.0
8 TraesCS4D01G134000 chr4B 91.201 2307 136 20 1898 4170 183608254 183605981 0.000000e+00 3073.0
9 TraesCS4D01G134000 chr4B 91.914 606 25 8 272 872 183612314 183611728 0.000000e+00 826.0
10 TraesCS4D01G134000 chr4B 92.172 511 40 0 954 1464 183608768 183608258 0.000000e+00 723.0
11 TraesCS4D01G134000 chr4B 90.850 306 8 7 1 286 183612635 183612330 4.580000e-105 392.0
12 TraesCS4D01G134000 chr4B 83.803 142 23 0 1 142 183672705 183672564 8.520000e-28 135.0
13 TraesCS4D01G134000 chr5D 96.192 709 26 1 4173 4880 483565080 483565788 0.000000e+00 1158.0
14 TraesCS4D01G134000 chr5D 95.499 711 26 4 4172 4880 549659960 549659254 0.000000e+00 1131.0
15 TraesCS4D01G134000 chr5D 79.002 581 93 20 385 957 347018232 347017673 2.150000e-98 370.0
16 TraesCS4D01G134000 chr7B 95.910 709 28 1 4173 4880 374311456 374312164 0.000000e+00 1147.0
17 TraesCS4D01G134000 chr3D 95.499 711 29 2 4171 4880 56302679 56303387 0.000000e+00 1133.0
18 TraesCS4D01G134000 chr3D 95.359 711 31 2 4171 4880 56308573 56309282 0.000000e+00 1129.0
19 TraesCS4D01G134000 chr3D 95.211 710 31 2 4172 4880 56287783 56288490 0.000000e+00 1120.0
20 TraesCS4D01G134000 chr2D 95.391 716 26 3 4171 4880 586288146 586287432 0.000000e+00 1133.0
21 TraesCS4D01G134000 chr2D 95.077 711 33 2 4172 4880 478050402 478051112 0.000000e+00 1118.0
22 TraesCS4D01G134000 chr2D 81.145 594 54 30 396 957 473101293 473100726 1.620000e-114 424.0
23 TraesCS4D01G134000 chr2D 77.581 678 98 33 306 957 547793409 547792760 1.290000e-95 361.0
24 TraesCS4D01G134000 chr2D 80.893 403 43 17 574 957 62386536 62386923 2.220000e-73 287.0
25 TraesCS4D01G134000 chr2B 80.862 580 71 33 396 957 552434689 552434132 2.100000e-113 420.0
26 TraesCS4D01G134000 chr2B 80.607 428 66 13 1474 1897 419553595 419554009 1.020000e-81 315.0
27 TraesCS4D01G134000 chr2B 79.343 426 71 11 1475 1897 415997279 415996868 2.880000e-72 283.0
28 TraesCS4D01G134000 chr6D 77.424 691 104 35 306 957 72223096 72223773 9.980000e-97 364.0
29 TraesCS4D01G134000 chr6D 84.746 236 26 9 472 703 436466241 436466012 1.370000e-55 228.0
30 TraesCS4D01G134000 chr2A 79.688 512 75 24 452 946 614585073 614584574 4.680000e-90 342.0
31 TraesCS4D01G134000 chr5B 81.455 426 62 13 1475 1897 340615291 340615702 2.810000e-87 333.0
32 TraesCS4D01G134000 chr5B 78.753 433 57 15 1475 1905 293509201 293508802 1.740000e-64 257.0
33 TraesCS4D01G134000 chr5B 84.184 196 19 5 1703 1897 391639051 391638867 3.880000e-41 180.0
34 TraesCS4D01G134000 chr5B 92.424 66 5 0 1832 1897 558417286 558417351 1.450000e-15 95.3
35 TraesCS4D01G134000 chr5A 80.886 429 60 15 1475 1897 460478182 460478594 7.880000e-83 318.0
36 TraesCS4D01G134000 chr5A 82.036 334 44 9 1475 1805 355171729 355172049 2.240000e-68 270.0
37 TraesCS4D01G134000 chr5A 77.701 435 74 17 539 957 112619077 112618650 1.360000e-60 244.0
38 TraesCS4D01G134000 chr5A 84.298 121 10 6 1767 1885 626219824 626219711 5.160000e-20 110.0
39 TraesCS4D01G134000 chr1D 79.758 331 46 12 1561 1891 205971637 205971328 2.290000e-53 220.0
40 TraesCS4D01G134000 chr6B 80.969 289 44 10 1476 1758 190176279 190176562 8.220000e-53 219.0
41 TraesCS4D01G134000 chr6A 82.051 234 25 9 472 703 584687667 584687449 3.000000e-42 183.0
42 TraesCS4D01G134000 chr3B 82.979 94 10 4 1782 1875 526803009 526803096 4.050000e-11 80.5
43 TraesCS4D01G134000 chr3A 100.000 28 0 0 1715 1742 60065724 60065751 9.000000e-03 52.8


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 TraesCS4D01G134000 chr4D 120881385 120886264 4879 True 9012.0 9012 100.00000 1 4880 1 chr4D.!!$R1 4879
1 TraesCS4D01G134000 chr4A 452346158 452350369 4211 True 3203.5 4416 93.71400 229 4138 2 chr4A.!!$R4 3909
2 TraesCS4D01G134000 chr4A 143443158 143443867 709 True 1122.0 1122 95.21100 4172 4880 1 chr4A.!!$R1 708
3 TraesCS4D01G134000 chr4B 183605981 183612635 6654 True 1253.5 3073 91.53425 1 4170 4 chr4B.!!$R2 4169
4 TraesCS4D01G134000 chr5D 483565080 483565788 708 False 1158.0 1158 96.19200 4173 4880 1 chr5D.!!$F1 707
5 TraesCS4D01G134000 chr5D 549659254 549659960 706 True 1131.0 1131 95.49900 4172 4880 1 chr5D.!!$R2 708
6 TraesCS4D01G134000 chr5D 347017673 347018232 559 True 370.0 370 79.00200 385 957 1 chr5D.!!$R1 572
7 TraesCS4D01G134000 chr7B 374311456 374312164 708 False 1147.0 1147 95.91000 4173 4880 1 chr7B.!!$F1 707
8 TraesCS4D01G134000 chr3D 56302679 56303387 708 False 1133.0 1133 95.49900 4171 4880 1 chr3D.!!$F2 709
9 TraesCS4D01G134000 chr3D 56308573 56309282 709 False 1129.0 1129 95.35900 4171 4880 1 chr3D.!!$F3 709
10 TraesCS4D01G134000 chr3D 56287783 56288490 707 False 1120.0 1120 95.21100 4172 4880 1 chr3D.!!$F1 708
11 TraesCS4D01G134000 chr2D 586287432 586288146 714 True 1133.0 1133 95.39100 4171 4880 1 chr2D.!!$R3 709
12 TraesCS4D01G134000 chr2D 478050402 478051112 710 False 1118.0 1118 95.07700 4172 4880 1 chr2D.!!$F2 708
13 TraesCS4D01G134000 chr2D 473100726 473101293 567 True 424.0 424 81.14500 396 957 1 chr2D.!!$R1 561
14 TraesCS4D01G134000 chr2D 547792760 547793409 649 True 361.0 361 77.58100 306 957 1 chr2D.!!$R2 651
15 TraesCS4D01G134000 chr2B 552434132 552434689 557 True 420.0 420 80.86200 396 957 1 chr2B.!!$R2 561
16 TraesCS4D01G134000 chr6D 72223096 72223773 677 False 364.0 364 77.42400 306 957 1 chr6D.!!$F1 651

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
725 843 1.202651 ACGACTTTAGGCTTGCTGTGT 60.203 47.619 0.00 0.0 0.00 3.72 F
1243 4259 0.248134 GCTACTCGTAGACAGCACCG 60.248 60.000 8.22 0.0 38.81 4.94 F
2578 5612 0.613260 TGCGGCTCCTGAACACTATT 59.387 50.000 0.00 0.0 0.00 1.73 F
3363 6709 1.270550 GTGCCTGTGGTGAATCAAAGG 59.729 52.381 0.00 0.0 43.44 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 5627 0.394216 ACAGTGCAACAGTCAAGGCA 60.394 50.0 0.00 0.00 41.43 4.75 R
3238 6582 0.682209 CAGCATGGCCTAGGCAAACT 60.682 55.0 34.09 21.91 42.43 2.66 R
3494 6847 0.770499 TGCCAGGGACTCATTTGACA 59.230 50.0 0.00 0.00 34.60 3.58 R
4325 7689 0.839946 ACTATGAGCGCCCCTTCATT 59.160 50.0 14.16 0.00 0.00 2.57 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
29 30 1.600916 GGCCGTTGATAGGGATGCC 60.601 63.158 0.00 0.00 0.00 4.40
159 166 4.247258 CAGCTCTGCCTGATGATTATCTC 58.753 47.826 0.00 0.00 34.77 2.75
217 224 3.578272 TTGTTGGTGCCACGCGAC 61.578 61.111 15.93 0.00 0.00 5.19
225 232 4.681978 GCCACGCGACCAAGGTCT 62.682 66.667 15.93 0.00 42.54 3.85
226 233 2.738521 CCACGCGACCAAGGTCTG 60.739 66.667 15.93 11.29 42.54 3.51
277 298 2.654863 ACCACACCAACAAAAGAGAGG 58.345 47.619 0.00 0.00 0.00 3.69
286 307 4.040952 CCAACAAAAGAGAGGGAGAGAGAA 59.959 45.833 0.00 0.00 0.00 2.87
709 827 2.391389 GCTGCCACCTGCTTACGAC 61.391 63.158 0.00 0.00 42.00 4.34
725 843 1.202651 ACGACTTTAGGCTTGCTGTGT 60.203 47.619 0.00 0.00 0.00 3.72
735 857 2.030805 GGCTTGCTGTGTTCCTTTGTAG 60.031 50.000 0.00 0.00 0.00 2.74
736 858 2.618709 GCTTGCTGTGTTCCTTTGTAGT 59.381 45.455 0.00 0.00 0.00 2.73
737 859 3.813166 GCTTGCTGTGTTCCTTTGTAGTA 59.187 43.478 0.00 0.00 0.00 1.82
966 3976 6.718912 TGTCATTGTCATATTGGTTTGAGGAA 59.281 34.615 0.00 0.00 0.00 3.36
987 3997 4.376340 AAGCAGAAAACAACAAGACCAG 57.624 40.909 0.00 0.00 0.00 4.00
1009 4019 0.248907 GAGACCGCGAATGGAATCGA 60.249 55.000 8.23 0.00 45.48 3.59
1134 4150 5.171339 TCTCTTTCAGATTTCTTCCCCTG 57.829 43.478 0.00 0.00 0.00 4.45
1151 4167 2.438434 GGACCGCATTCCCTGGTG 60.438 66.667 0.00 0.00 35.75 4.17
1243 4259 0.248134 GCTACTCGTAGACAGCACCG 60.248 60.000 8.22 0.00 38.81 4.94
1291 4307 1.626654 CGTAGACCACAAGCTTGCCG 61.627 60.000 26.27 17.88 0.00 5.69
1323 4339 2.754658 CTGCCCGACCTCTACCGT 60.755 66.667 0.00 0.00 0.00 4.83
1432 4448 3.610477 CGCTGCTCATACTCTGCG 58.390 61.111 0.00 0.00 42.33 5.18
1639 4657 6.937436 AAAATACCAGGAAATGTATCCGTC 57.063 37.500 0.00 0.00 44.60 4.79
1730 4749 9.793259 TTTTGTCTTCTTTACTGAGAATACCAT 57.207 29.630 0.00 0.00 35.27 3.55
1736 4755 7.437713 TCTTTACTGAGAATACCATGGATGT 57.562 36.000 21.47 2.18 0.00 3.06
1743 4762 7.616935 ACTGAGAATACCATGGATGTCATTTTT 59.383 33.333 21.47 0.00 32.92 1.94
1746 4765 7.775120 AGAATACCATGGATGTCATTTTTCAC 58.225 34.615 21.47 0.00 32.92 3.18
1756 4775 6.142320 GGATGTCATTTTTCACGAAACTTCAC 59.858 38.462 0.00 0.00 0.00 3.18
1757 4776 5.944013 TGTCATTTTTCACGAAACTTCACA 58.056 33.333 0.00 0.00 0.00 3.58
1758 4777 6.382608 TGTCATTTTTCACGAAACTTCACAA 58.617 32.000 0.00 0.00 0.00 3.33
1759 4778 6.526325 TGTCATTTTTCACGAAACTTCACAAG 59.474 34.615 0.00 0.00 0.00 3.16
1760 4779 6.020678 GTCATTTTTCACGAAACTTCACAAGG 60.021 38.462 0.00 0.00 0.00 3.61
1761 4780 4.364415 TTTTCACGAAACTTCACAAGGG 57.636 40.909 0.00 0.00 0.00 3.95
1762 4781 2.702592 TCACGAAACTTCACAAGGGT 57.297 45.000 0.00 0.00 0.00 4.34
1774 4793 2.158219 TCACAAGGGTCAAGGGAGTAGA 60.158 50.000 0.00 0.00 0.00 2.59
2128 5148 9.292195 CCTTTAAACTAACTCAACCCATCTTTA 57.708 33.333 0.00 0.00 0.00 1.85
2206 5240 4.649674 GTCTACAACAGGAGATGGGTGATA 59.350 45.833 0.00 0.00 0.00 2.15
2578 5612 0.613260 TGCGGCTCCTGAACACTATT 59.387 50.000 0.00 0.00 0.00 1.73
2896 6240 7.881643 TCAATTACACCAAAATGTGCATTAC 57.118 32.000 0.00 0.00 39.93 1.89
2920 6264 8.655935 ACTTTAGGATTTGGATTTGTTCTCAT 57.344 30.769 0.00 0.00 0.00 2.90
2993 6337 4.008330 AGGACAGCATATGCATATTCAGC 58.992 43.478 28.62 16.33 45.16 4.26
2997 6341 2.745821 AGCATATGCATATTCAGCGTGG 59.254 45.455 28.62 4.45 45.16 4.94
3014 6358 3.772932 CGTGGATTAATGCAAACATGCT 58.227 40.909 11.58 0.00 36.36 3.79
3161 6505 7.447374 AATGCTAAGCACTTACATTGTTGTA 57.553 32.000 12.97 0.00 43.04 2.41
3212 6556 2.813100 GCGAAAACAAGCCCATGTG 58.187 52.632 0.00 0.00 32.81 3.21
3280 6626 8.034215 GCTGCTAGAGACTTGATTGTATATGAT 58.966 37.037 0.00 0.00 0.00 2.45
3345 6691 1.421646 ACCAAGGGAGAGAGGTTTGTG 59.578 52.381 0.00 0.00 0.00 3.33
3363 6709 1.270550 GTGCCTGTGGTGAATCAAAGG 59.729 52.381 0.00 0.00 43.44 3.11
3366 6712 1.888512 CCTGTGGTGAATCAAAGGTGG 59.111 52.381 0.00 0.00 37.37 4.61
3494 6847 2.348998 CTGCGAGGAAACCAGCCT 59.651 61.111 0.00 0.00 38.81 4.58
3588 6941 0.237235 GCGATGAGTTTGGCGAAACA 59.763 50.000 23.75 6.99 43.51 2.83
3599 6952 3.315796 CGAAACACGCGTTCAGGT 58.684 55.556 10.22 0.13 32.91 4.00
3634 6987 5.119898 GCGCTCTACATTCTTTGGATATCAG 59.880 44.000 0.00 0.00 0.00 2.90
3665 7018 5.450550 CCTCTTCTTTCACAAACCCAAGTTC 60.451 44.000 0.00 0.00 34.19 3.01
3707 7060 3.977244 GGTGTGGCGTTTGGCTGG 61.977 66.667 0.00 0.00 42.94 4.85
3712 7065 1.896660 TGGCGTTTGGCTGGAGAAC 60.897 57.895 0.00 0.00 42.94 3.01
3713 7066 1.896660 GGCGTTTGGCTGGAGAACA 60.897 57.895 0.00 0.00 42.94 3.18
3714 7067 1.452145 GGCGTTTGGCTGGAGAACAA 61.452 55.000 0.00 0.00 42.94 2.83
3720 7073 4.676723 CGTTTGGCTGGAGAACAAGAAAAA 60.677 41.667 0.00 0.00 0.00 1.94
3736 7089 6.882678 ACAAGAAAAACTAACTAGTGGTGTGT 59.117 34.615 0.00 0.00 36.50 3.72
3737 7090 8.042515 ACAAGAAAAACTAACTAGTGGTGTGTA 58.957 33.333 0.00 0.00 36.50 2.90
3861 7214 1.892474 GAGAAGAGCAGACTGTGGACT 59.108 52.381 3.99 0.00 0.00 3.85
3914 7267 1.655350 GCTGCTGTGTTGTGCGTTC 60.655 57.895 0.00 0.00 0.00 3.95
3924 7277 3.924073 GTGTTGTGCGTTCCTTTCTTTTT 59.076 39.130 0.00 0.00 0.00 1.94
3947 7300 6.892658 TTTACAGTTGCTGTATCATTTGGT 57.107 33.333 9.44 0.00 44.85 3.67
4057 7419 3.632643 ATTTCATTTTCATGGTGGGGC 57.367 42.857 0.00 0.00 0.00 5.80
4065 7427 4.601406 TTTCATGGTGGGGCTACTTAAT 57.399 40.909 0.00 0.00 0.00 1.40
4066 7428 4.601406 TTCATGGTGGGGCTACTTAATT 57.399 40.909 0.00 0.00 0.00 1.40
4067 7429 4.601406 TCATGGTGGGGCTACTTAATTT 57.399 40.909 0.00 0.00 0.00 1.82
4068 7430 4.277476 TCATGGTGGGGCTACTTAATTTG 58.723 43.478 0.00 0.00 0.00 2.32
4142 7504 8.814038 AGGATATTGATGTTCTTAAAGTTGCT 57.186 30.769 0.00 0.00 0.00 3.91
4145 7507 4.145876 TGATGTTCTTAAAGTTGCTGCG 57.854 40.909 0.00 0.00 0.00 5.18
4146 7508 2.399396 TGTTCTTAAAGTTGCTGCGC 57.601 45.000 0.00 0.00 0.00 6.09
4150 7512 2.426522 TCTTAAAGTTGCTGCGCAGAT 58.573 42.857 40.21 19.33 40.61 2.90
4232 7595 3.649986 GCGATGCATACGGCCACC 61.650 66.667 16.56 0.00 43.89 4.61
4256 7619 9.628500 ACCTTATTAATTATTCTCACAAGACCC 57.372 33.333 0.00 0.00 0.00 4.46
4307 7671 2.612212 CCACGTCTAAGCAACAACTGTT 59.388 45.455 0.00 0.00 39.12 3.16
4325 7689 6.808321 ACTGTTGCTACTCCTATCCAATTA 57.192 37.500 0.00 0.00 0.00 1.40
4339 7703 1.338020 CCAATTAATGAAGGGGCGCTC 59.662 52.381 7.64 1.18 0.00 5.03
4402 7766 6.500336 ACCTAAACATCTAAGACCTGAGGTA 58.500 40.000 2.97 0.00 35.25 3.08
4447 7811 3.702048 GCACCTACCAGTCCGGCA 61.702 66.667 0.00 0.00 39.03 5.69
4552 7916 3.710722 CTTGCCCGGCCTCTCTGT 61.711 66.667 7.03 0.00 0.00 3.41
4661 8030 2.750888 GCCGAGAAACGCCACCATC 61.751 63.158 0.00 0.00 41.07 3.51
4742 8111 2.894765 TGTACACCTCCAAGAATGACGA 59.105 45.455 0.00 0.00 0.00 4.20
4773 8142 1.448985 AACGACACAATAATGCCGCT 58.551 45.000 0.00 0.00 0.00 5.52
4848 8217 0.792640 AACTTCTCAACAGCGATGCG 59.207 50.000 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.961277 GCATCCCTATCAACGGCCG 60.961 63.158 26.86 26.86 0.00 6.13
16 17 0.320683 CGCATCGGCATCCCTATCAA 60.321 55.000 0.00 0.00 41.24 2.57
29 30 4.637489 CTCTCCTCCGCCGCATCG 62.637 72.222 0.00 0.00 0.00 3.84
76 83 3.371063 GGGACGTCCTGAGCGTGA 61.371 66.667 32.52 0.00 43.04 4.35
159 166 0.618458 TTCCCAAATCCACCGGAGAG 59.382 55.000 9.46 0.00 34.05 3.20
225 232 1.960040 AATCGATGCGGCTGGTCTCA 61.960 55.000 0.00 0.00 0.00 3.27
226 233 1.218230 GAATCGATGCGGCTGGTCTC 61.218 60.000 0.00 0.00 0.00 3.36
299 350 1.460273 TTTCTTCCGGCCCAACTTGC 61.460 55.000 0.00 0.00 0.00 4.01
402 463 1.139734 GCAGTCGCGAGGAGAATCA 59.860 57.895 10.24 0.00 36.25 2.57
682 788 4.357947 GGTGGCAGCACGACGAGA 62.358 66.667 12.58 0.00 0.00 4.04
709 827 2.508526 AGGAACACAGCAAGCCTAAAG 58.491 47.619 0.00 0.00 0.00 1.85
966 3976 3.131046 CCTGGTCTTGTTGTTTTCTGCTT 59.869 43.478 0.00 0.00 0.00 3.91
987 3997 0.105039 ATTCCATTCGCGGTCTCTCC 59.895 55.000 6.13 0.00 0.00 3.71
1009 4019 1.957562 CTGCTGCTGCTGCTTCTTT 59.042 52.632 27.67 0.00 40.48 2.52
1134 4150 2.438434 CACCAGGGAATGCGGTCC 60.438 66.667 0.00 0.00 36.90 4.46
1243 4259 5.888161 AGAAGTATTGGGATGTGGATTTGTC 59.112 40.000 0.00 0.00 0.00 3.18
1536 4553 5.423610 TCCAGGTGTTTTTGAATTTTCCTGA 59.576 36.000 9.09 0.00 42.33 3.86
1639 4657 0.921347 CGGAGTGTATTTCCTTCGCG 59.079 55.000 0.00 0.00 32.34 5.87
1708 4726 7.556844 TCCATGGTATTCTCAGTAAAGAAGAC 58.443 38.462 12.58 3.46 43.49 3.01
1709 4727 7.733773 TCCATGGTATTCTCAGTAAAGAAGA 57.266 36.000 12.58 0.00 38.60 2.87
1710 4728 7.989741 ACATCCATGGTATTCTCAGTAAAGAAG 59.010 37.037 12.58 0.00 38.60 2.85
1711 4729 7.861629 ACATCCATGGTATTCTCAGTAAAGAA 58.138 34.615 12.58 0.00 39.49 2.52
1713 4731 7.275183 TGACATCCATGGTATTCTCAGTAAAG 58.725 38.462 12.58 0.00 0.00 1.85
1730 4749 5.766150 AGTTTCGTGAAAAATGACATCCA 57.234 34.783 0.00 0.00 31.33 3.41
1736 4755 6.033341 CCTTGTGAAGTTTCGTGAAAAATGA 58.967 36.000 0.00 0.00 31.33 2.57
1743 4762 2.093394 TGACCCTTGTGAAGTTTCGTGA 60.093 45.455 0.00 0.00 0.00 4.35
1746 4765 2.290641 CCTTGACCCTTGTGAAGTTTCG 59.709 50.000 0.00 0.00 34.31 3.46
1756 4775 3.370953 CCAATCTACTCCCTTGACCCTTG 60.371 52.174 0.00 0.00 0.00 3.61
1757 4776 2.846827 CCAATCTACTCCCTTGACCCTT 59.153 50.000 0.00 0.00 0.00 3.95
1758 4777 2.482494 CCAATCTACTCCCTTGACCCT 58.518 52.381 0.00 0.00 0.00 4.34
1759 4778 1.490910 CCCAATCTACTCCCTTGACCC 59.509 57.143 0.00 0.00 0.00 4.46
1760 4779 2.197465 ACCCAATCTACTCCCTTGACC 58.803 52.381 0.00 0.00 0.00 4.02
1761 4780 3.134262 GGTACCCAATCTACTCCCTTGAC 59.866 52.174 0.00 0.00 0.00 3.18
1762 4781 3.381335 GGTACCCAATCTACTCCCTTGA 58.619 50.000 0.00 0.00 0.00 3.02
2378 5412 3.551890 ACTGTTCATAGCTAATCGCGTTG 59.448 43.478 5.77 0.00 45.59 4.10
2379 5413 3.551890 CACTGTTCATAGCTAATCGCGTT 59.448 43.478 5.77 2.26 45.59 4.84
2409 5443 9.213777 AGATGGAGTAAAGTAAACCTATCATCA 57.786 33.333 0.00 0.00 31.50 3.07
2410 5444 9.482627 CAGATGGAGTAAAGTAAACCTATCATC 57.517 37.037 0.00 0.00 0.00 2.92
2541 5575 2.284952 CGCATACAAGATCACGAATGCA 59.715 45.455 17.63 0.00 39.68 3.96
2578 5612 7.829211 ACAGTCAAGGCAAAGATTAAAGCTATA 59.171 33.333 0.00 0.00 0.00 1.31
2593 5627 0.394216 ACAGTGCAACAGTCAAGGCA 60.394 50.000 0.00 0.00 41.43 4.75
2655 5690 5.083533 ACTCATCTAGCACCTTCAAGAAG 57.916 43.478 2.83 2.83 38.14 2.85
2725 5760 1.296715 CCCTGCGGTAGTGAAAGCT 59.703 57.895 0.00 0.00 0.00 3.74
2752 5787 6.150140 ACAGTGCAAGCTAAAGAAATAAGGAG 59.850 38.462 0.00 0.00 0.00 3.69
2819 5854 6.542005 AGCGGTTGATATGACATAACATTGAA 59.458 34.615 6.28 0.00 0.00 2.69
2920 6264 7.004555 AGTGCCGATACAGAATATTGGAATA 57.995 36.000 4.62 0.00 31.46 1.75
2938 6282 1.737793 GAAAACAGGGTATGAGTGCCG 59.262 52.381 0.00 0.00 0.00 5.69
2977 6321 2.743664 TCCACGCTGAATATGCATATGC 59.256 45.455 21.09 21.09 42.50 3.14
3238 6582 0.682209 CAGCATGGCCTAGGCAAACT 60.682 55.000 34.09 21.91 42.43 2.66
3280 6626 2.104792 CACCTCAGTTCCTCCTGTTTGA 59.895 50.000 0.00 0.00 34.02 2.69
3345 6691 1.270550 CACCTTTGATTCACCACAGGC 59.729 52.381 0.00 0.00 37.48 4.85
3363 6709 4.885325 CACAACCCCCAGTAATAATACCAC 59.115 45.833 0.00 0.00 32.08 4.16
3366 6712 5.820947 CAGTCACAACCCCCAGTAATAATAC 59.179 44.000 0.00 0.00 0.00 1.89
3415 6768 1.092921 TGGTTCCACAACGACTGCAC 61.093 55.000 0.00 0.00 32.68 4.57
3494 6847 0.770499 TGCCAGGGACTCATTTGACA 59.230 50.000 0.00 0.00 34.60 3.58
3588 6941 3.165160 AAGCTCCACCTGAACGCGT 62.165 57.895 5.58 5.58 0.00 6.01
3665 7018 8.964150 CCATAATCAATATATGCATCGCAATTG 58.036 33.333 0.19 9.38 43.62 2.32
3707 7060 8.336080 CACCACTAGTTAGTTTTTCTTGTTCTC 58.664 37.037 0.00 0.00 33.46 2.87
3712 7065 7.316544 ACACACCACTAGTTAGTTTTTCTTG 57.683 36.000 0.00 0.00 33.46 3.02
3713 7066 9.623000 ATTACACACCACTAGTTAGTTTTTCTT 57.377 29.630 0.00 0.00 33.46 2.52
3714 7067 9.052759 CATTACACACCACTAGTTAGTTTTTCT 57.947 33.333 0.00 0.00 33.46 2.52
3720 7073 8.617809 CAAAAACATTACACACCACTAGTTAGT 58.382 33.333 0.00 0.00 36.90 2.24
3762 7115 2.668212 TTCCCTTTCACTGCCGCG 60.668 61.111 0.00 0.00 0.00 6.46
3768 7121 2.373502 CTCTTCCACCTTCCCTTTCACT 59.626 50.000 0.00 0.00 0.00 3.41
3861 7214 2.854963 ACTCAGCAGTGAAGCAAATGA 58.145 42.857 0.00 0.00 36.85 2.57
3940 7293 7.281774 AGCTCAATGATCTAACACTACCAAATG 59.718 37.037 0.00 0.00 0.00 2.32
3946 7299 6.481984 GCAAAGCTCAATGATCTAACACTAC 58.518 40.000 0.00 0.00 0.00 2.73
3947 7300 5.291858 CGCAAAGCTCAATGATCTAACACTA 59.708 40.000 0.00 0.00 0.00 2.74
4057 7419 7.712797 ACCACAGGAACAAACAAATTAAGTAG 58.287 34.615 0.00 0.00 0.00 2.57
4065 7427 6.568869 CAAGAATACCACAGGAACAAACAAA 58.431 36.000 0.00 0.00 0.00 2.83
4066 7428 5.451242 GCAAGAATACCACAGGAACAAACAA 60.451 40.000 0.00 0.00 0.00 2.83
4067 7429 4.037446 GCAAGAATACCACAGGAACAAACA 59.963 41.667 0.00 0.00 0.00 2.83
4068 7430 4.546570 GCAAGAATACCACAGGAACAAAC 58.453 43.478 0.00 0.00 0.00 2.93
4142 7504 3.118775 ACAAGGTTCAGTATATCTGCGCA 60.119 43.478 10.98 10.98 43.32 6.09
4145 7507 5.581085 ACGAAACAAGGTTCAGTATATCTGC 59.419 40.000 0.00 0.00 43.32 4.26
4146 7508 6.590292 ACACGAAACAAGGTTCAGTATATCTG 59.410 38.462 0.00 0.00 44.85 2.90
4150 7512 7.556733 AAAACACGAAACAAGGTTCAGTATA 57.443 32.000 0.00 0.00 0.00 1.47
4307 7671 7.453393 CCTTCATTAATTGGATAGGAGTAGCA 58.547 38.462 0.00 0.00 0.00 3.49
4325 7689 0.839946 ACTATGAGCGCCCCTTCATT 59.160 50.000 14.16 0.00 0.00 2.57
4339 7703 4.974645 TTGGTATTAGGCCCAGACTATG 57.025 45.455 0.00 0.00 31.04 2.23
4552 7916 3.366915 TCGTGGTGGCGTCGATGA 61.367 61.111 9.31 0.00 0.00 2.92
4661 8030 2.223409 CGGTGATTCATCCTGCACATTG 60.223 50.000 0.00 0.00 33.09 2.82
4742 8111 1.208535 TGTGTCGTTTCCCTCTTGTGT 59.791 47.619 0.00 0.00 0.00 3.72
4848 8217 1.332686 GGTGTCGTTCCCTTGTTGAAC 59.667 52.381 0.00 0.00 38.95 3.18


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

AutoCloner maintained by Alex Coulton.