Multiple sequence alignment - TraesCS7A01G114300

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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 TraesCS7A01G114300 chr7A 100.000 2649 0 0 1 2649 70248699 70246051 0.000000e+00 4892.0
1 TraesCS7A01G114300 chr7A 84.825 1173 120 25 476 1604 74856382 74857540 0.000000e+00 1127.0
2 TraesCS7A01G114300 chr7A 85.953 719 56 27 859 1554 70194799 70195495 0.000000e+00 726.0
3 TraesCS7A01G114300 chr7A 80.808 891 93 34 1593 2455 70214994 70214154 6.220000e-176 627.0
4 TraesCS7A01G114300 chr7A 88.780 508 36 4 1606 2113 74857640 74858126 1.050000e-168 603.0
5 TraesCS7A01G114300 chr7A 92.899 338 14 4 2322 2649 70196244 70196581 1.430000e-132 483.0
6 TraesCS7A01G114300 chr7A 78.143 851 111 45 811 1600 74592304 74593140 3.090000e-129 472.0
7 TraesCS7A01G114300 chr7A 86.308 409 53 2 3 411 74855977 74856382 2.420000e-120 442.0
8 TraesCS7A01G114300 chr7A 81.285 529 54 23 1593 2113 70195699 70196190 1.150000e-103 387.0
9 TraesCS7A01G114300 chr7A 77.260 708 99 28 932 1603 70898563 70897882 2.510000e-95 359.0
10 TraesCS7A01G114300 chr7A 76.694 738 95 37 1702 2389 70237158 70236448 3.270000e-89 339.0
11 TraesCS7A01G114300 chr7A 76.657 664 112 23 859 1488 85199072 85198418 7.070000e-86 327.0
12 TraesCS7A01G114300 chr7A 88.489 278 17 4 2385 2649 74858448 74858723 3.290000e-84 322.0
13 TraesCS7A01G114300 chr7A 88.938 226 11 5 2165 2389 74858208 74858420 1.560000e-67 267.0
14 TraesCS7A01G114300 chr7A 85.652 230 16 5 774 986 70233799 70233570 2.650000e-55 226.0
15 TraesCS7A01G114300 chr7A 78.893 289 33 19 2382 2649 70266253 70265972 1.260000e-38 171.0
16 TraesCS7A01G114300 chr7A 87.770 139 13 4 854 992 86466398 86466532 2.730000e-35 159.0
17 TraesCS7A01G114300 chr7A 80.603 232 22 9 1389 1604 70215362 70215138 9.820000e-35 158.0
18 TraesCS7A01G114300 chr7A 87.770 139 9 7 2515 2649 85197084 85196950 3.530000e-34 156.0
19 TraesCS7A01G114300 chr7A 86.364 132 15 2 2518 2649 70734467 70734339 9.890000e-30 141.0
20 TraesCS7A01G114300 chr7A 86.364 132 15 2 2518 2649 74687075 74687203 9.890000e-30 141.0
21 TraesCS7A01G114300 chr7A 78.696 230 29 12 1693 1908 74742518 74742741 4.600000e-28 135.0
22 TraesCS7A01G114300 chr7D 88.233 2660 167 52 3 2616 65825393 65822834 0.000000e+00 3044.0
23 TraesCS7A01G114300 chr7D 83.855 830 57 33 813 1604 65814745 65813955 0.000000e+00 719.0
24 TraesCS7A01G114300 chr7D 90.619 501 23 11 2165 2649 65792746 65792254 0.000000e+00 643.0
25 TraesCS7A01G114300 chr7D 79.322 856 97 46 811 1603 68901754 68902592 6.490000e-146 527.0
26 TraesCS7A01G114300 chr7D 75.140 893 131 48 773 1600 66548276 66547410 4.230000e-88 335.0
27 TraesCS7A01G114300 chr7D 74.134 866 154 47 763 1600 68897360 68898183 7.170000e-76 294.0
28 TraesCS7A01G114300 chr7D 82.857 245 13 9 1907 2150 65793015 65792799 2.690000e-45 193.0
29 TraesCS7A01G114300 chr7D 77.698 278 54 7 367 642 258233563 258233834 2.110000e-36 163.0
30 TraesCS7A01G114300 chr7D 86.364 132 15 2 2518 2649 69043795 69043923 9.890000e-30 141.0
31 TraesCS7A01G114300 chr7B 84.235 425 52 12 811 1230 10067478 10067892 1.480000e-107 399.0
32 TraesCS7A01G114300 chr7B 76.857 700 97 34 932 1598 7732392 7731725 4.230000e-88 335.0
33 TraesCS7A01G114300 chr7B 74.440 536 78 29 1101 1599 10061113 10061626 2.710000e-40 176.0
34 TraesCS7A01G114300 chr7B 83.051 118 8 8 1489 1600 10559598 10559709 2.170000e-16 97.1
35 TraesCS7A01G114300 chr6D 84.772 197 7 9 790 968 473377691 473377882 2.710000e-40 176.0
36 TraesCS7A01G114300 chr6D 81.319 91 15 2 541 630 377218089 377218000 3.660000e-09 73.1
37 TraesCS7A01G114300 chr3B 77.778 270 50 8 368 629 13456874 13456607 9.820000e-35 158.0
38 TraesCS7A01G114300 chr2B 77.174 276 45 11 362 629 767708183 767707918 7.640000e-31 145.0
39 TraesCS7A01G114300 chr2B 76.812 276 46 11 362 629 767741056 767740791 3.560000e-29 139.0
40 TraesCS7A01G114300 chr4B 75.273 275 61 4 363 630 172792102 172792376 9.960000e-25 124.0
41 TraesCS7A01G114300 chr2A 76.339 224 44 7 414 630 527370510 527370731 7.750000e-21 111.0
42 TraesCS7A01G114300 chr2A 82.222 90 13 3 541 629 756481246 756481333 1.020000e-09 75.0
43 TraesCS7A01G114300 chr2D 88.043 92 8 3 541 630 610865046 610864956 3.610000e-19 106.0
44 TraesCS7A01G114300 chr5A 85.263 95 13 1 537 630 364426796 364426890 2.170000e-16 97.1
45 TraesCS7A01G114300 chr1A 76.596 188 34 7 451 630 12794865 12795050 7.810000e-16 95.3


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 TraesCS7A01G114300 chr7A 70246051 70248699 2648 True 4892.0 4892 100.000000 1 2649 1 chr7A.!!$R1 2648
1 TraesCS7A01G114300 chr7A 74855977 74858723 2746 False 552.2 1127 87.468000 3 2649 5 chr7A.!!$F6 2646
2 TraesCS7A01G114300 chr7A 70194799 70196581 1782 False 532.0 726 86.712333 859 2649 3 chr7A.!!$F5 1790
3 TraesCS7A01G114300 chr7A 74592304 74593140 836 False 472.0 472 78.143000 811 1600 1 chr7A.!!$F1 789
4 TraesCS7A01G114300 chr7A 70214154 70215362 1208 True 392.5 627 80.705500 1389 2455 2 chr7A.!!$R5 1066
5 TraesCS7A01G114300 chr7A 70897882 70898563 681 True 359.0 359 77.260000 932 1603 1 chr7A.!!$R4 671
6 TraesCS7A01G114300 chr7A 70233570 70237158 3588 True 282.5 339 81.173000 774 2389 2 chr7A.!!$R6 1615
7 TraesCS7A01G114300 chr7A 85196950 85199072 2122 True 241.5 327 82.213500 859 2649 2 chr7A.!!$R7 1790
8 TraesCS7A01G114300 chr7D 65822834 65825393 2559 True 3044.0 3044 88.233000 3 2616 1 chr7D.!!$R2 2613
9 TraesCS7A01G114300 chr7D 65813955 65814745 790 True 719.0 719 83.855000 813 1604 1 chr7D.!!$R1 791
10 TraesCS7A01G114300 chr7D 65792254 65793015 761 True 418.0 643 86.738000 1907 2649 2 chr7D.!!$R4 742
11 TraesCS7A01G114300 chr7D 68897360 68902592 5232 False 410.5 527 76.728000 763 1603 2 chr7D.!!$F3 840
12 TraesCS7A01G114300 chr7D 66547410 66548276 866 True 335.0 335 75.140000 773 1600 1 chr7D.!!$R3 827
13 TraesCS7A01G114300 chr7B 7731725 7732392 667 True 335.0 335 76.857000 932 1598 1 chr7B.!!$R1 666

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
692 725 0.042731 TTCCCCCTTCCGAGACATCT 59.957 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 4824 0.324738 TTGAGGGCCTCGATCTCACT 60.325 55.0 27.58 0.0 37.28 3.41 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
41 42 4.377839 GCCCAAAGCTTAGAATTTCTCC 57.622 45.455 0.00 0.00 38.99 3.71
43 44 4.261801 CCCAAAGCTTAGAATTTCTCCGA 58.738 43.478 0.00 0.00 0.00 4.55
87 88 4.456222 CCACACTACTATAGACCCTCATCG 59.544 50.000 6.78 0.00 0.00 3.84
99 100 3.664025 CTCATCGCCGCCAAGTGGA 62.664 63.158 0.18 0.00 34.74 4.02
112 113 2.043652 GTGGAGCCATGCCCATGT 60.044 61.111 7.42 0.00 37.11 3.21
123 124 1.229177 GCCCATGTGGAGGGGTTTT 60.229 57.895 0.00 0.00 45.90 2.43
133 134 6.555463 TGTGGAGGGGTTTTAGTATTAGAG 57.445 41.667 0.00 0.00 0.00 2.43
141 142 5.221402 GGGTTTTAGTATTAGAGGGGAGACG 60.221 48.000 0.00 0.00 0.00 4.18
144 145 7.449704 GGTTTTAGTATTAGAGGGGAGACGATA 59.550 40.741 0.00 0.00 0.00 2.92
241 242 2.035632 GCTGAGAGCCCACATAGTAGT 58.964 52.381 0.00 0.00 34.48 2.73
310 311 3.640407 ACAGTCCCAGCGCACCAT 61.640 61.111 11.47 0.00 0.00 3.55
340 341 3.306166 CGTTTCATGGGAGCTTAGTAACG 59.694 47.826 0.00 0.00 0.00 3.18
363 364 6.976925 ACGTAAGGTCGTTTCTTCTAATATGG 59.023 38.462 0.00 0.00 41.37 2.74
364 365 6.976925 CGTAAGGTCGTTTCTTCTAATATGGT 59.023 38.462 0.00 0.00 0.00 3.55
411 412 4.299586 TCTATGCAAGGGTTCAATGACA 57.700 40.909 0.00 0.00 0.00 3.58
419 420 1.069227 GGGTTCAATGACAACGACTGC 60.069 52.381 0.00 0.00 0.00 4.40
422 423 0.867746 TCAATGACAACGACTGCAGC 59.132 50.000 15.27 5.81 0.00 5.25
448 449 2.565841 GGCGCTGATCCTTAAAGACAT 58.434 47.619 7.64 0.00 0.00 3.06
473 474 0.435008 CGAAGACTTTTCGGCTGTCG 59.565 55.000 0.00 0.00 38.19 4.35
474 475 1.499049 GAAGACTTTTCGGCTGTCGT 58.501 50.000 0.09 0.00 40.32 4.34
498 499 1.617947 AAGGTCAAGCCGGCTCTAGG 61.618 60.000 32.93 19.55 43.70 3.02
499 500 2.501610 GTCAAGCCGGCTCTAGGG 59.498 66.667 32.93 16.91 0.00 3.53
500 501 2.058595 GTCAAGCCGGCTCTAGGGA 61.059 63.158 32.93 18.99 0.00 4.20
527 533 1.200484 ACAAAGTGCGTTGACGGTTTT 59.800 42.857 5.62 0.00 40.23 2.43
551 557 1.303091 GGCGGCATTAGTGGTCGTTT 61.303 55.000 3.07 0.00 0.00 3.60
553 559 1.434555 CGGCATTAGTGGTCGTTTGA 58.565 50.000 0.00 0.00 0.00 2.69
675 708 9.118236 CTGGAGAAAGAAAAACACGATATTTTC 57.882 33.333 12.84 12.84 42.88 2.29
676 709 8.079809 TGGAGAAAGAAAAACACGATATTTTCC 58.920 33.333 15.40 0.00 43.33 3.13
682 715 5.654603 AAAACACGATATTTTCCCCCTTC 57.345 39.130 0.00 0.00 0.00 3.46
690 723 1.368374 TTTTCCCCCTTCCGAGACAT 58.632 50.000 0.00 0.00 0.00 3.06
692 725 0.042731 TTCCCCCTTCCGAGACATCT 59.957 55.000 0.00 0.00 0.00 2.90
723 756 2.637025 TTTTTCAGCGCCGACAGC 59.363 55.556 2.29 0.00 38.52 4.40
724 757 2.183504 TTTTTCAGCGCCGACAGCA 61.184 52.632 2.29 0.00 44.04 4.41
725 758 1.719725 TTTTTCAGCGCCGACAGCAA 61.720 50.000 2.29 0.00 44.04 3.91
726 759 2.116736 TTTTCAGCGCCGACAGCAAG 62.117 55.000 2.29 0.00 44.04 4.01
727 760 3.807631 TTCAGCGCCGACAGCAAGT 62.808 57.895 2.29 0.00 44.04 3.16
728 761 3.349006 CAGCGCCGACAGCAAGTT 61.349 61.111 2.29 0.00 44.04 2.66
729 762 3.349006 AGCGCCGACAGCAAGTTG 61.349 61.111 2.29 0.00 44.04 3.16
730 763 3.345808 GCGCCGACAGCAAGTTGA 61.346 61.111 7.16 0.00 44.04 3.18
731 764 2.680913 GCGCCGACAGCAAGTTGAT 61.681 57.895 7.16 0.00 44.04 2.57
732 765 1.868997 CGCCGACAGCAAGTTGATT 59.131 52.632 7.16 0.00 44.04 2.57
733 766 0.238289 CGCCGACAGCAAGTTGATTT 59.762 50.000 7.16 0.00 44.04 2.17
734 767 1.334960 CGCCGACAGCAAGTTGATTTT 60.335 47.619 7.16 0.00 44.04 1.82
735 768 2.742774 GCCGACAGCAAGTTGATTTTT 58.257 42.857 7.16 0.00 42.97 1.94
737 770 3.550842 GCCGACAGCAAGTTGATTTTTCT 60.551 43.478 7.16 0.00 42.97 2.52
738 771 4.610945 CCGACAGCAAGTTGATTTTTCTT 58.389 39.130 7.16 0.00 33.04 2.52
739 772 5.043248 CCGACAGCAAGTTGATTTTTCTTT 58.957 37.500 7.16 0.00 33.04 2.52
740 773 5.519927 CCGACAGCAAGTTGATTTTTCTTTT 59.480 36.000 7.16 0.00 33.04 2.27
742 775 6.253298 CGACAGCAAGTTGATTTTTCTTTTGA 59.747 34.615 7.16 0.00 33.04 2.69
743 776 7.514125 CGACAGCAAGTTGATTTTTCTTTTGAG 60.514 37.037 7.16 0.00 33.04 3.02
744 777 7.322664 ACAGCAAGTTGATTTTTCTTTTGAGA 58.677 30.769 7.16 0.00 0.00 3.27
746 779 7.276218 CAGCAAGTTGATTTTTCTTTTGAGACA 59.724 33.333 7.16 0.00 0.00 3.41
747 780 7.818930 AGCAAGTTGATTTTTCTTTTGAGACAA 59.181 29.630 7.16 0.00 0.00 3.18
908 3515 0.180406 AACCGTCTCAACCAACAGCT 59.820 50.000 0.00 0.00 0.00 4.24
1208 3858 3.207669 CTACGGGCGCTACCTCGT 61.208 66.667 7.64 12.29 44.33 4.18
1299 3961 2.164219 CGAGGCAATGTTTTGGTATGCT 59.836 45.455 0.00 0.00 37.20 3.79
1537 4265 3.601435 TCTCCCGAATTTGCACGAATTA 58.399 40.909 0.00 0.00 29.75 1.40
1540 4268 2.422127 CCCGAATTTGCACGAATTAGGT 59.578 45.455 16.91 0.00 39.02 3.08
1541 4269 3.119637 CCCGAATTTGCACGAATTAGGTT 60.120 43.478 16.91 0.00 39.02 3.50
1542 4270 4.095610 CCGAATTTGCACGAATTAGGTTC 58.904 43.478 12.44 0.00 37.15 3.62
1680 4621 4.374702 CCGAACGTCGTCGACCGT 62.375 66.667 19.29 16.46 43.86 4.83
1700 4642 2.026262 GTGGCTCATTCTGGTTTAGGGA 60.026 50.000 0.00 0.00 0.00 4.20
1714 4656 0.679002 TAGGGAGAGGTCCGTGTTCG 60.679 60.000 0.00 0.00 45.05 3.95
1779 4733 0.036952 ACCTCGTCATGTGCTTCCAG 60.037 55.000 0.00 0.00 0.00 3.86
1841 4795 4.660938 AAACCACCAGCCCCTCGC 62.661 66.667 0.00 0.00 37.98 5.03
1917 4913 7.239438 TCCTACTCTTCTTCCTAGTCTTGAAA 58.761 38.462 0.00 0.00 0.00 2.69
2022 5073 1.486310 ACTGAAACTGGTGCAGTCTGA 59.514 47.619 0.00 0.00 44.62 3.27
2023 5074 2.092968 ACTGAAACTGGTGCAGTCTGAA 60.093 45.455 0.00 0.00 44.62 3.02
2024 5075 2.945008 CTGAAACTGGTGCAGTCTGAAA 59.055 45.455 3.32 0.00 44.62 2.69
2026 5077 2.717639 AACTGGTGCAGTCTGAAACT 57.282 45.000 3.32 0.00 44.62 2.66
2027 5078 2.717639 ACTGGTGCAGTCTGAAACTT 57.282 45.000 3.32 0.00 41.21 2.66
2028 5079 2.565841 ACTGGTGCAGTCTGAAACTTC 58.434 47.619 3.32 0.00 41.21 3.01
2029 5080 2.171448 ACTGGTGCAGTCTGAAACTTCT 59.829 45.455 3.32 0.00 41.21 2.85
2030 5081 3.209410 CTGGTGCAGTCTGAAACTTCTT 58.791 45.455 3.32 0.00 35.45 2.52
2031 5082 4.141711 ACTGGTGCAGTCTGAAACTTCTTA 60.142 41.667 3.32 0.00 41.21 2.10
2032 5083 4.973168 TGGTGCAGTCTGAAACTTCTTAT 58.027 39.130 3.32 0.00 35.45 1.73
2033 5084 4.997395 TGGTGCAGTCTGAAACTTCTTATC 59.003 41.667 3.32 0.00 35.45 1.75
2034 5085 5.221722 TGGTGCAGTCTGAAACTTCTTATCT 60.222 40.000 3.32 0.00 35.45 1.98
2035 5086 5.121454 GGTGCAGTCTGAAACTTCTTATCTG 59.879 44.000 3.32 0.00 35.45 2.90
2036 5087 5.698545 GTGCAGTCTGAAACTTCTTATCTGT 59.301 40.000 3.32 0.00 35.45 3.41
2037 5088 6.203723 GTGCAGTCTGAAACTTCTTATCTGTT 59.796 38.462 3.32 0.00 35.45 3.16
2038 5089 6.767902 TGCAGTCTGAAACTTCTTATCTGTTT 59.232 34.615 3.32 0.00 35.45 2.83
2039 5090 7.041780 TGCAGTCTGAAACTTCTTATCTGTTTC 60.042 37.037 3.32 9.90 45.51 2.78
2074 5132 9.110502 GTTAGGAGTTAGGACTTGGAAATATTG 57.889 37.037 0.00 0.00 35.88 1.90
2113 5171 6.313519 AGGATTACAGGCATCAGTAAAAGA 57.686 37.500 0.00 0.00 34.27 2.52
2114 5172 6.116126 AGGATTACAGGCATCAGTAAAAGAC 58.884 40.000 0.00 0.00 34.27 3.01
2115 5173 6.069963 AGGATTACAGGCATCAGTAAAAGACT 60.070 38.462 0.00 0.00 39.82 3.24
2116 5174 7.125811 AGGATTACAGGCATCAGTAAAAGACTA 59.874 37.037 0.00 0.00 35.64 2.59
2117 5175 7.769044 GGATTACAGGCATCAGTAAAAGACTAA 59.231 37.037 0.00 0.00 35.64 2.24
2118 5176 9.162764 GATTACAGGCATCAGTAAAAGACTAAA 57.837 33.333 0.00 0.00 35.64 1.85
2119 5177 8.911918 TTACAGGCATCAGTAAAAGACTAAAA 57.088 30.769 0.00 0.00 35.64 1.52
2120 5178 7.440523 ACAGGCATCAGTAAAAGACTAAAAG 57.559 36.000 0.00 0.00 35.64 2.27
2150 5228 7.092079 TGAATCAAATCCACAATGAACATGTC 58.908 34.615 0.00 0.00 0.00 3.06
2152 5230 4.518590 TCAAATCCACAATGAACATGTCGT 59.481 37.500 0.00 0.00 0.00 4.34
2158 5236 7.674471 TCCACAATGAACATGTCGTAATAAA 57.326 32.000 0.00 0.00 0.00 1.40
2159 5237 8.100508 TCCACAATGAACATGTCGTAATAAAA 57.899 30.769 0.00 0.00 0.00 1.52
2161 5239 8.020819 CCACAATGAACATGTCGTAATAAAAGT 58.979 33.333 0.00 0.00 0.00 2.66
2162 5240 9.393249 CACAATGAACATGTCGTAATAAAAGTT 57.607 29.630 0.00 0.00 0.00 2.66
2163 5241 9.393249 ACAATGAACATGTCGTAATAAAAGTTG 57.607 29.630 0.00 0.00 0.00 3.16
2299 5695 8.219105 ACTGTAATTTCTTTCGAATAACGTGTC 58.781 33.333 0.00 0.00 43.13 3.67
2320 5716 7.360607 CGTGTCGTAAAATTCAGGTTTTATCCT 60.361 37.037 0.00 0.00 36.34 3.24
2327 5723 6.759497 AATTCAGGTTTTATCCTACAGCAC 57.241 37.500 0.00 0.00 35.87 4.40
2328 5724 4.901197 TCAGGTTTTATCCTACAGCACA 57.099 40.909 0.00 0.00 35.87 4.57
2600 6094 4.422057 TGTCCCTGACAGTATAGGAAACA 58.578 43.478 0.93 6.29 37.67 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153549 GGCTCTTCGAGGCGACAAT 60.154 57.895 0.00 0.00 44.75 2.71
1 2 2.261671 GGCTCTTCGAGGCGACAA 59.738 61.111 0.00 0.00 44.75 3.18
33 34 3.429547 CGACATGGACTCTCGGAGAAATT 60.430 47.826 9.32 0.00 34.09 1.82
37 38 0.035343 ACGACATGGACTCTCGGAGA 60.035 55.000 7.60 7.60 33.32 3.71
64 65 4.456222 CGATGAGGGTCTATAGTAGTGTGG 59.544 50.000 0.00 0.00 0.00 4.17
71 72 1.535833 CGGCGATGAGGGTCTATAGT 58.464 55.000 0.00 0.00 0.00 2.12
99 100 2.277737 CTCCACATGGGCATGGCT 59.722 61.111 19.78 0.00 42.91 4.75
112 113 4.973211 CCCTCTAATACTAAAACCCCTCCA 59.027 45.833 0.00 0.00 0.00 3.86
123 124 6.499699 TCACTATCGTCTCCCCTCTAATACTA 59.500 42.308 0.00 0.00 0.00 1.82
133 134 2.034812 GTCATGTCACTATCGTCTCCCC 59.965 54.545 0.00 0.00 0.00 4.81
141 142 4.496341 CGCCCATTTTGTCATGTCACTATC 60.496 45.833 0.00 0.00 0.00 2.08
144 145 1.541147 CGCCCATTTTGTCATGTCACT 59.459 47.619 0.00 0.00 0.00 3.41
154 155 1.474077 CCTTCCTCTTCGCCCATTTTG 59.526 52.381 0.00 0.00 0.00 2.44
156 157 0.681243 GCCTTCCTCTTCGCCCATTT 60.681 55.000 0.00 0.00 0.00 2.32
241 242 2.110213 GCCCGTTGGTGTGTCTGA 59.890 61.111 0.00 0.00 0.00 3.27
310 311 0.690192 TCCCATGAAACGAAGGCTCA 59.310 50.000 0.00 0.00 0.00 4.26
340 341 9.807649 TTACCATATTAGAAGAAACGACCTTAC 57.192 33.333 0.00 0.00 0.00 2.34
357 358 8.790718 GCATCTGACATCAAATCTTACCATATT 58.209 33.333 0.00 0.00 0.00 1.28
363 364 7.279536 TCTCAAGCATCTGACATCAAATCTTAC 59.720 37.037 0.00 0.00 0.00 2.34
364 365 7.333323 TCTCAAGCATCTGACATCAAATCTTA 58.667 34.615 0.00 0.00 0.00 2.10
373 374 5.221661 TGCATAGATCTCAAGCATCTGACAT 60.222 40.000 11.32 0.00 32.61 3.06
380 381 3.137913 ACCCTTGCATAGATCTCAAGCAT 59.862 43.478 14.35 4.80 36.72 3.79
411 412 1.293498 CCCTAGTGCTGCAGTCGTT 59.707 57.895 16.64 1.54 0.00 3.85
422 423 1.040646 TAAGGATCAGCGCCCTAGTG 58.959 55.000 2.29 0.00 31.36 2.74
448 449 0.934496 CCGAAAAGTCTTCGTGCACA 59.066 50.000 18.64 0.81 40.04 4.57
473 474 2.027625 CCGGCTTGACCTTGTCGAC 61.028 63.158 9.11 9.11 34.95 4.20
474 475 2.342279 CCGGCTTGACCTTGTCGA 59.658 61.111 0.00 0.00 34.95 4.20
498 499 4.090057 GCACTTTGTCGCCGCTCC 62.090 66.667 0.00 0.00 0.00 4.70
499 500 4.430423 CGCACTTTGTCGCCGCTC 62.430 66.667 0.00 0.00 0.00 5.03
504 505 1.717728 CGTCAACGCACTTTGTCGC 60.718 57.895 0.00 0.00 32.72 5.19
506 507 0.375803 AACCGTCAACGCACTTTGTC 59.624 50.000 0.00 0.00 38.18 3.18
507 508 0.806241 AAACCGTCAACGCACTTTGT 59.194 45.000 0.00 0.00 38.18 2.83
508 509 1.902840 AAAACCGTCAACGCACTTTG 58.097 45.000 0.00 0.00 38.18 2.77
527 533 0.540830 ACCACTAATGCCGCCCAAAA 60.541 50.000 0.00 0.00 0.00 2.44
530 536 2.270850 GACCACTAATGCCGCCCA 59.729 61.111 0.00 0.00 0.00 5.36
531 537 2.895372 CGACCACTAATGCCGCCC 60.895 66.667 0.00 0.00 0.00 6.13
551 557 0.899019 TCGGGATTCGAACACCATCA 59.101 50.000 20.01 5.23 45.86 3.07
641 674 7.041721 GTGTTTTTCTTTCTCCAGGAAACATT 58.958 34.615 3.03 0.00 38.81 2.71
648 681 6.743575 ATATCGTGTTTTTCTTTCTCCAGG 57.256 37.500 0.00 0.00 0.00 4.45
651 684 7.541091 GGGAAAATATCGTGTTTTTCTTTCTCC 59.459 37.037 14.37 7.24 40.21 3.71
675 708 2.128729 GAGATGTCTCGGAAGGGGG 58.871 63.158 0.00 0.00 32.78 5.40
711 744 3.349006 AACTTGCTGTCGGCGCTG 61.349 61.111 10.86 10.86 45.43 5.18
718 751 7.489113 TCTCAAAAGAAAAATCAACTTGCTGTC 59.511 33.333 0.00 0.00 0.00 3.51
719 752 7.276438 GTCTCAAAAGAAAAATCAACTTGCTGT 59.724 33.333 0.00 0.00 31.93 4.40
720 753 7.276218 TGTCTCAAAAGAAAAATCAACTTGCTG 59.724 33.333 0.00 0.00 31.93 4.41
721 754 7.322664 TGTCTCAAAAGAAAAATCAACTTGCT 58.677 30.769 0.00 0.00 31.93 3.91
722 755 7.524294 TGTCTCAAAAGAAAAATCAACTTGC 57.476 32.000 0.00 0.00 31.93 4.01
723 756 9.357652 TCTTGTCTCAAAAGAAAAATCAACTTG 57.642 29.630 0.00 0.00 31.93 3.16
724 757 9.358872 GTCTTGTCTCAAAAGAAAAATCAACTT 57.641 29.630 0.00 0.00 35.50 2.66
725 758 8.522830 TGTCTTGTCTCAAAAGAAAAATCAACT 58.477 29.630 0.00 0.00 35.50 3.16
726 759 8.687824 TGTCTTGTCTCAAAAGAAAAATCAAC 57.312 30.769 0.00 0.00 35.50 3.18
727 760 7.489113 GCTGTCTTGTCTCAAAAGAAAAATCAA 59.511 33.333 0.00 0.00 35.50 2.57
728 761 6.974622 GCTGTCTTGTCTCAAAAGAAAAATCA 59.025 34.615 0.00 0.00 35.50 2.57
729 762 6.974622 TGCTGTCTTGTCTCAAAAGAAAAATC 59.025 34.615 0.00 0.00 35.50 2.17
730 763 6.866480 TGCTGTCTTGTCTCAAAAGAAAAAT 58.134 32.000 0.00 0.00 35.50 1.82
731 764 6.266168 TGCTGTCTTGTCTCAAAAGAAAAA 57.734 33.333 0.00 0.00 35.50 1.94
732 765 5.895636 TGCTGTCTTGTCTCAAAAGAAAA 57.104 34.783 0.00 0.00 35.50 2.29
733 766 5.415701 ACTTGCTGTCTTGTCTCAAAAGAAA 59.584 36.000 0.00 0.00 35.50 2.52
734 767 4.943705 ACTTGCTGTCTTGTCTCAAAAGAA 59.056 37.500 0.00 0.00 35.50 2.52
735 768 4.517285 ACTTGCTGTCTTGTCTCAAAAGA 58.483 39.130 0.00 0.00 0.00 2.52
737 770 4.699735 TCAACTTGCTGTCTTGTCTCAAAA 59.300 37.500 0.00 0.00 0.00 2.44
738 771 4.260985 TCAACTTGCTGTCTTGTCTCAAA 58.739 39.130 0.00 0.00 0.00 2.69
739 772 3.872696 TCAACTTGCTGTCTTGTCTCAA 58.127 40.909 0.00 0.00 0.00 3.02
740 773 3.541996 TCAACTTGCTGTCTTGTCTCA 57.458 42.857 0.00 0.00 0.00 3.27
742 775 4.077300 TCATCAACTTGCTGTCTTGTCT 57.923 40.909 0.00 0.00 0.00 3.41
743 776 5.368256 AATCATCAACTTGCTGTCTTGTC 57.632 39.130 0.00 0.00 0.00 3.18
744 777 5.413833 CCTAATCATCAACTTGCTGTCTTGT 59.586 40.000 0.00 0.00 0.00 3.16
746 779 4.397417 GCCTAATCATCAACTTGCTGTCTT 59.603 41.667 0.00 0.00 0.00 3.01
747 780 3.944015 GCCTAATCATCAACTTGCTGTCT 59.056 43.478 0.00 0.00 0.00 3.41
908 3515 1.005924 GGGAGAAGATGGGAAGCCAAA 59.994 52.381 0.00 0.00 0.00 3.28
1299 3961 2.669133 CCCGGATTCTGACAGGGCA 61.669 63.158 0.73 0.00 36.15 5.36
1537 4265 1.072331 ACGCACATCCAAGAAGAACCT 59.928 47.619 0.00 0.00 0.00 3.50
1540 4268 1.428448 CGACGCACATCCAAGAAGAA 58.572 50.000 0.00 0.00 0.00 2.52
1541 4269 0.389817 CCGACGCACATCCAAGAAGA 60.390 55.000 0.00 0.00 0.00 2.87
1542 4270 0.389817 TCCGACGCACATCCAAGAAG 60.390 55.000 0.00 0.00 0.00 2.85
1680 4621 2.239654 CTCCCTAAACCAGAATGAGCCA 59.760 50.000 0.00 0.00 39.69 4.75
1700 4642 1.228490 AGGTCGAACACGGACCTCT 60.228 57.895 1.87 0.00 45.35 3.69
1714 4656 2.716017 CCAGCTCGTCCCTCAGGTC 61.716 68.421 0.00 0.00 0.00 3.85
1779 4733 1.876156 GTAAGCCAGGCAGCATATGTC 59.124 52.381 15.80 0.00 34.23 3.06
1841 4795 2.286559 GCGATGACGACGACGATGG 61.287 63.158 15.32 0.49 42.66 3.51
1870 4824 0.324738 TTGAGGGCCTCGATCTCACT 60.325 55.000 27.58 0.00 37.28 3.41
1917 4913 4.653341 TGAAACCCAAAACATCTGGACAAT 59.347 37.500 0.00 0.00 35.85 2.71
2022 5073 9.495572 CTCCTAACTGAAACAGATAAGAAGTTT 57.504 33.333 5.76 0.00 38.10 2.66
2023 5074 8.652290 ACTCCTAACTGAAACAGATAAGAAGTT 58.348 33.333 5.76 0.00 35.18 2.66
2024 5075 8.196378 ACTCCTAACTGAAACAGATAAGAAGT 57.804 34.615 5.76 0.00 35.18 3.01
2027 5078 8.750298 CCTAACTCCTAACTGAAACAGATAAGA 58.250 37.037 5.76 0.00 35.18 2.10
2028 5079 8.750298 TCCTAACTCCTAACTGAAACAGATAAG 58.250 37.037 5.76 0.65 35.18 1.73
2029 5080 8.660295 TCCTAACTCCTAACTGAAACAGATAA 57.340 34.615 5.76 0.00 35.18 1.75
2030 5081 7.894364 ACTCCTAACTCCTAACTGAAACAGATA 59.106 37.037 5.76 0.00 35.18 1.98
2031 5082 6.726764 ACTCCTAACTCCTAACTGAAACAGAT 59.273 38.462 5.76 0.00 35.18 2.90
2032 5083 6.075984 ACTCCTAACTCCTAACTGAAACAGA 58.924 40.000 5.76 0.00 35.18 3.41
2033 5084 6.347859 ACTCCTAACTCCTAACTGAAACAG 57.652 41.667 0.00 0.00 37.52 3.16
2034 5085 6.742559 AACTCCTAACTCCTAACTGAAACA 57.257 37.500 0.00 0.00 0.00 2.83
2035 5086 7.178097 TCCTAACTCCTAACTCCTAACTGAAAC 59.822 40.741 0.00 0.00 0.00 2.78
2036 5087 7.178097 GTCCTAACTCCTAACTCCTAACTGAAA 59.822 40.741 0.00 0.00 0.00 2.69
2037 5088 6.662663 GTCCTAACTCCTAACTCCTAACTGAA 59.337 42.308 0.00 0.00 0.00 3.02
2038 5089 6.011805 AGTCCTAACTCCTAACTCCTAACTGA 60.012 42.308 0.00 0.00 0.00 3.41
2039 5090 6.189133 AGTCCTAACTCCTAACTCCTAACTG 58.811 44.000 0.00 0.00 0.00 3.16
2040 5091 6.405872 AGTCCTAACTCCTAACTCCTAACT 57.594 41.667 0.00 0.00 0.00 2.24
2041 5092 6.127394 CCAAGTCCTAACTCCTAACTCCTAAC 60.127 46.154 0.00 0.00 33.48 2.34
2042 5093 5.956563 CCAAGTCCTAACTCCTAACTCCTAA 59.043 44.000 0.00 0.00 33.48 2.69
2043 5094 5.254737 TCCAAGTCCTAACTCCTAACTCCTA 59.745 44.000 0.00 0.00 33.48 2.94
2044 5095 4.045590 TCCAAGTCCTAACTCCTAACTCCT 59.954 45.833 0.00 0.00 33.48 3.69
2045 5096 4.351127 TCCAAGTCCTAACTCCTAACTCC 58.649 47.826 0.00 0.00 33.48 3.85
2046 5097 5.997384 TTCCAAGTCCTAACTCCTAACTC 57.003 43.478 0.00 0.00 33.48 3.01
2074 5132 2.099141 TCCTACAGCATGCAGTTCAC 57.901 50.000 21.46 0.00 42.53 3.18
2113 5171 7.147976 GTGGATTTGATTCAGCAACTTTTAGT 58.852 34.615 0.00 0.00 0.00 2.24
2114 5172 7.147312 TGTGGATTTGATTCAGCAACTTTTAG 58.853 34.615 0.00 0.00 0.00 1.85
2115 5173 7.048629 TGTGGATTTGATTCAGCAACTTTTA 57.951 32.000 0.00 0.00 0.00 1.52
2116 5174 5.916318 TGTGGATTTGATTCAGCAACTTTT 58.084 33.333 0.00 0.00 0.00 2.27
2117 5175 5.534207 TGTGGATTTGATTCAGCAACTTT 57.466 34.783 0.00 0.00 0.00 2.66
2118 5176 5.534207 TTGTGGATTTGATTCAGCAACTT 57.466 34.783 0.00 0.00 0.00 2.66
2119 5177 5.244402 TCATTGTGGATTTGATTCAGCAACT 59.756 36.000 0.00 0.00 0.00 3.16
2120 5178 5.472148 TCATTGTGGATTTGATTCAGCAAC 58.528 37.500 0.00 0.00 0.00 4.17
2150 5228 6.655062 TCAGTGTTCAGCAACTTTTATTACG 58.345 36.000 0.00 0.00 33.17 3.18
2158 5236 8.097038 TCTTTCTATATCAGTGTTCAGCAACTT 58.903 33.333 0.00 0.00 33.17 2.66
2159 5237 7.615403 TCTTTCTATATCAGTGTTCAGCAACT 58.385 34.615 0.00 0.00 33.17 3.16
2161 5239 8.721478 GTTTCTTTCTATATCAGTGTTCAGCAA 58.279 33.333 0.00 0.00 0.00 3.91
2162 5240 8.097038 AGTTTCTTTCTATATCAGTGTTCAGCA 58.903 33.333 0.00 0.00 0.00 4.41
2163 5241 8.485976 AGTTTCTTTCTATATCAGTGTTCAGC 57.514 34.615 0.00 0.00 0.00 4.26
2262 5658 7.692705 CGAAAGAAATTACAGTAGGCTAAAAGC 59.307 37.037 0.00 0.00 41.46 3.51
2263 5659 8.932791 TCGAAAGAAATTACAGTAGGCTAAAAG 58.067 33.333 0.00 0.00 37.03 2.27
2283 5679 7.736880 TGAATTTTACGACACGTTATTCGAAAG 59.263 33.333 15.75 0.00 41.54 2.62
2299 5695 7.908601 GCTGTAGGATAAAACCTGAATTTTACG 59.091 37.037 0.00 0.00 40.81 3.18
2320 5716 7.213216 ACATCAAAACAATGTATGTGCTGTA 57.787 32.000 0.00 0.00 42.99 2.74
2328 5724 8.977505 GCTGTACAAAACATCAAAACAATGTAT 58.022 29.630 0.00 0.00 36.35 2.29


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

AutoCloner maintained by Alex Coulton.