Multiple sequence alignment - TraesCS6D01G109600

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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 TraesCS6D01G109600 chr6D 100.000 2918 0 0 1 2918 75371314 75374231 0.000000e+00 5389.0
1 TraesCS6D01G109600 chr6D 94.065 674 40 0 1229 1902 75372314 75372987 0.000000e+00 1024.0
2 TraesCS6D01G109600 chr6D 94.065 674 40 0 1001 1674 75372542 75373215 0.000000e+00 1024.0
3 TraesCS6D01G109600 chr6A 92.920 1370 63 15 1 1359 91422724 91424070 0.000000e+00 1962.0
4 TraesCS6D01G109600 chr6A 94.335 812 24 10 1639 2447 91424352 91425144 0.000000e+00 1225.0
5 TraesCS6D01G109600 chr6A 96.241 133 5 0 2472 2604 91425774 91425906 4.900000e-53 219.0
6 TraesCS6D01G109600 chr6A 94.262 122 7 0 2761 2882 91426034 91426155 1.380000e-43 187.0
7 TraesCS6D01G109600 chr6A 91.358 81 1 2 2607 2681 91425957 91426037 3.980000e-19 106.0
8 TraesCS6D01G109600 chr6A 100.000 32 0 0 2444 2475 91425730 91425761 3.140000e-05 60.2
9 TraesCS6D01G109600 chr6A 100.000 32 0 0 2887 2918 91426186 91426217 3.140000e-05 60.2
10 TraesCS6D01G109600 chr6B 89.215 1057 81 12 1229 2272 149055185 149056221 0.000000e+00 1290.0
11 TraesCS6D01G109600 chr6B 91.267 813 67 3 864 1674 149055048 149055858 0.000000e+00 1105.0
12 TraesCS6D01G109600 chr6B 84.311 784 50 27 1 773 149054327 149055048 0.000000e+00 699.0
13 TraesCS6D01G109600 chr6B 87.221 493 57 6 957 1446 171972072 171971583 9.130000e-155 556.0
14 TraesCS6D01G109600 chr6B 83.616 177 22 5 1 175 171973029 171972858 3.010000e-35 159.0
15 TraesCS6D01G109600 chr6B 100.000 38 0 0 2773 2810 149056421 149056458 1.450000e-08 71.3
16 TraesCS6D01G109600 chr7D 88.985 926 102 0 998 1923 562149189 562148264 0.000000e+00 1146.0
17 TraesCS6D01G109600 chr7A 88.851 879 98 0 1010 1888 647307230 647306352 0.000000e+00 1081.0
18 TraesCS6D01G109600 chr7A 89.640 444 46 0 998 1441 648042810 648042367 1.520000e-157 566.0
19 TraesCS6D01G109600 chrUn 89.928 695 68 2 1229 1922 20705504 20706197 0.000000e+00 894.0
20 TraesCS6D01G109600 chr2D 88.022 743 86 2 933 1674 520583592 520582852 0.000000e+00 876.0
21 TraesCS6D01G109600 chr2D 88.811 715 74 5 1229 1941 520583523 520582813 0.000000e+00 872.0
22 TraesCS6D01G109600 chr2D 84.444 180 20 8 3 176 520584530 520584353 1.390000e-38 171.0
23 TraesCS6D01G109600 chr2D 92.233 103 5 3 2678 2779 131465388 131465288 3.030000e-30 143.0
24 TraesCS6D01G109600 chr2D 90.566 106 8 2 2660 2765 31708391 31708494 3.920000e-29 139.0
25 TraesCS6D01G109600 chr2B 89.670 455 46 1 933 1386 613037734 613037280 1.950000e-161 579.0
26 TraesCS6D01G109600 chr2B 88.197 305 19 10 1983 2279 575947658 575947363 5.980000e-92 348.0
27 TraesCS6D01G109600 chr2B 84.831 178 18 7 3 176 613038619 613038447 1.390000e-38 171.0
28 TraesCS6D01G109600 chr2B 90.152 132 10 2 2143 2272 214277956 214278086 5.000000e-38 169.0
29 TraesCS6D01G109600 chr2B 95.082 61 3 0 2483 2543 214278116 214278176 2.390000e-16 97.1
30 TraesCS6D01G109600 chr1B 87.043 301 25 3 1979 2272 415854293 415854586 7.800000e-86 327.0
31 TraesCS6D01G109600 chr1B 94.737 95 4 1 2674 2768 391911509 391911602 2.340000e-31 147.0
32 TraesCS6D01G109600 chr1B 98.361 61 1 0 2483 2543 654865301 654865361 1.110000e-19 108.0
33 TraesCS6D01G109600 chr1B 84.615 104 12 3 2486 2587 48532035 48532136 1.850000e-17 100.0
34 TraesCS6D01G109600 chr7B 89.394 132 11 2 2143 2272 123030599 123030729 2.330000e-36 163.0
35 TraesCS6D01G109600 chr7B 87.879 132 13 2 2143 2272 122952579 122952709 5.040000e-33 152.0
36 TraesCS6D01G109600 chr7B 98.361 61 1 0 2483 2543 122952739 122952799 1.110000e-19 108.0
37 TraesCS6D01G109600 chr7B 98.361 61 1 0 2483 2543 123030759 123030819 1.110000e-19 108.0
38 TraesCS6D01G109600 chr5D 95.699 93 2 2 2674 2765 223231456 223231365 6.520000e-32 148.0
39 TraesCS6D01G109600 chr3A 95.699 93 3 1 2674 2765 221948899 221948991 6.520000e-32 148.0
40 TraesCS6D01G109600 chr3D 94.681 94 5 0 2673 2766 602232034 602231941 2.340000e-31 147.0
41 TraesCS6D01G109600 chr3D 88.235 119 12 2 2656 2773 571378058 571377941 1.090000e-29 141.0
42 TraesCS6D01G109600 chr4B 93.000 100 6 1 2667 2766 166003059 166003157 8.430000e-31 145.0
43 TraesCS6D01G109600 chr4D 91.262 103 7 2 2667 2769 476207216 476207116 3.920000e-29 139.0
44 TraesCS6D01G109600 chr3B 84.746 118 11 5 2486 2599 607501166 607501052 8.550000e-21 111.0
45 TraesCS6D01G109600 chr4A 98.387 62 1 0 2483 2544 660220872 660220933 3.070000e-20 110.0


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 TraesCS6D01G109600 chr6D 75371314 75374231 2917 False 2479.000000 5389 96.043333 1 2918 3 chr6D.!!$F1 2917
1 TraesCS6D01G109600 chr6A 91422724 91426217 3493 False 545.628571 1962 95.588000 1 2918 7 chr6A.!!$F1 2917
2 TraesCS6D01G109600 chr6B 149054327 149056458 2131 False 791.325000 1290 91.198250 1 2810 4 chr6B.!!$F1 2809
3 TraesCS6D01G109600 chr6B 171971583 171973029 1446 True 357.500000 556 85.418500 1 1446 2 chr6B.!!$R1 1445
4 TraesCS6D01G109600 chr7D 562148264 562149189 925 True 1146.000000 1146 88.985000 998 1923 1 chr7D.!!$R1 925
5 TraesCS6D01G109600 chr7A 647306352 647307230 878 True 1081.000000 1081 88.851000 1010 1888 1 chr7A.!!$R1 878
6 TraesCS6D01G109600 chrUn 20705504 20706197 693 False 894.000000 894 89.928000 1229 1922 1 chrUn.!!$F1 693
7 TraesCS6D01G109600 chr2D 520582813 520584530 1717 True 639.666667 876 87.092333 3 1941 3 chr2D.!!$R2 1938
8 TraesCS6D01G109600 chr2B 613037280 613038619 1339 True 375.000000 579 87.250500 3 1386 2 chr2B.!!$R2 1383

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
198 212 0.307760 CTTTTTGAGGTGCTTCGCGT 59.692 50.0 5.77 0.0 0.00 6.01 F
1305 1575 0.784178 CTGACACCATCGACAACGTG 59.216 55.0 0.00 0.0 40.69 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 1752 0.518636 CAAGTGTGATGGTCTTGCCG 59.481 55.0 0.0 0.0 41.21 5.69 R
2625 4245 0.898320 AGAATCGTCCCCACAGACAG 59.102 55.0 0.0 0.0 36.52 3.51 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
88 102 2.106683 CCAACCAATCTCGTCGCCC 61.107 63.158 0.00 0.00 0.00 6.13
178 192 4.313282 CCCACGTATCGTCTAGATCTACA 58.687 47.826 0.00 0.00 38.32 2.74
198 212 0.307760 CTTTTTGAGGTGCTTCGCGT 59.692 50.000 5.77 0.00 0.00 6.01
211 225 0.889994 TTCGCGTTAGTTGGAGCCTA 59.110 50.000 5.77 0.00 0.00 3.93
306 357 1.585668 CTATTCGCGCACAGAGACTTG 59.414 52.381 8.75 0.00 0.00 3.16
346 397 1.061711 CTCGCGATTTCTTTCCTGCTG 59.938 52.381 10.36 0.00 0.00 4.41
347 398 0.798776 CGCGATTTCTTTCCTGCTGT 59.201 50.000 0.00 0.00 0.00 4.40
348 399 1.197721 CGCGATTTCTTTCCTGCTGTT 59.802 47.619 0.00 0.00 0.00 3.16
349 400 2.350772 CGCGATTTCTTTCCTGCTGTTT 60.351 45.455 0.00 0.00 0.00 2.83
350 401 3.642705 GCGATTTCTTTCCTGCTGTTTT 58.357 40.909 0.00 0.00 0.00 2.43
351 402 4.051237 GCGATTTCTTTCCTGCTGTTTTT 58.949 39.130 0.00 0.00 0.00 1.94
398 453 3.563808 TGTTCGTCTTGGTTGAATTCCTG 59.436 43.478 2.27 0.00 0.00 3.86
414 469 2.763039 TCCTGATGGCTTATGGTCTCA 58.237 47.619 0.00 0.00 0.00 3.27
423 481 6.252599 TGGCTTATGGTCTCAGATGTTAAT 57.747 37.500 0.00 0.00 0.00 1.40
424 482 6.057533 TGGCTTATGGTCTCAGATGTTAATG 58.942 40.000 0.00 0.00 0.00 1.90
448 510 9.730705 ATGTATGCATGTTTTATCTGCTAGTAT 57.269 29.630 10.16 0.00 36.84 2.12
486 619 5.611197 CGAATTCAATAGTAGCTCATGTGCG 60.611 44.000 13.68 0.00 38.13 5.34
572 781 6.780522 TCACCCAAAGCTTAGGTTTATTTTCT 59.219 34.615 16.50 0.00 31.81 2.52
573 782 7.289084 TCACCCAAAGCTTAGGTTTATTTTCTT 59.711 33.333 16.50 0.00 31.81 2.52
574 783 8.581578 CACCCAAAGCTTAGGTTTATTTTCTTA 58.418 33.333 16.50 0.00 31.81 2.10
575 784 8.803235 ACCCAAAGCTTAGGTTTATTTTCTTAG 58.197 33.333 13.96 0.00 31.81 2.18
576 785 9.020731 CCCAAAGCTTAGGTTTATTTTCTTAGA 57.979 33.333 9.15 0.00 31.81 2.10
626 835 3.455910 TGTGGAACCCTTGAGATAGATGG 59.544 47.826 0.00 0.00 34.36 3.51
631 840 5.336849 GGAACCCTTGAGATAGATGGTATCG 60.337 48.000 0.00 0.00 0.00 2.92
686 915 6.567050 TCTTTGATGAAGAAAATATGCTGCC 58.433 36.000 0.00 0.00 41.34 4.85
687 916 4.924305 TGATGAAGAAAATATGCTGCCC 57.076 40.909 0.00 0.00 0.00 5.36
688 917 3.638160 TGATGAAGAAAATATGCTGCCCC 59.362 43.478 0.00 0.00 0.00 5.80
706 935 1.131693 CCCCCGTTTGTTTATTCTCGC 59.868 52.381 0.00 0.00 0.00 5.03
750 979 6.049149 ACGTGCTAATAGTTATTGCACATCT 58.951 36.000 23.30 12.36 43.13 2.90
751 980 7.207383 ACGTGCTAATAGTTATTGCACATCTA 58.793 34.615 23.30 0.00 43.13 1.98
752 981 7.709182 ACGTGCTAATAGTTATTGCACATCTAA 59.291 33.333 23.30 0.00 43.13 2.10
760 997 6.109359 AGTTATTGCACATCTAAGTGACTCC 58.891 40.000 0.00 0.00 42.05 3.85
784 1021 9.323985 TCCATCAAACATAAAAAGGAAAACAAG 57.676 29.630 0.00 0.00 0.00 3.16
860 1098 7.011482 GGACTTAAGATGTGCAATACTTAGGTG 59.989 40.741 19.33 11.59 36.07 4.00
930 1168 8.398665 GCTTTATGTATAGGGCTGCATTATTAC 58.601 37.037 0.50 0.00 0.00 1.89
1074 1344 2.153247 GTCGTCTGACACAATCGACAAC 59.847 50.000 8.73 0.00 46.28 3.32
1131 1401 1.520342 GGACCAGCAGCGTCTCATC 60.520 63.158 1.07 0.00 0.00 2.92
1221 1491 2.815647 CTTGTCCTCCGCCTTCGC 60.816 66.667 0.00 0.00 0.00 4.70
1305 1575 0.784178 CTGACACCATCGACAACGTG 59.216 55.000 0.00 0.00 40.69 4.49
1317 1587 1.880027 GACAACGTGAAGGCCAAGATT 59.120 47.619 5.01 0.00 0.00 2.40
1449 1719 1.265454 ACCTTGTCCTCCGCCTTAGG 61.265 60.000 0.00 0.00 35.26 2.69
1470 1740 1.216122 GAGGCATGCAGATCTTCGTC 58.784 55.000 21.36 0.00 0.00 4.20
1482 1752 0.966920 TCTTCGTCAAGACCCTCACC 59.033 55.000 0.00 0.00 33.38 4.02
1494 1764 1.450312 CCTCACCGGCAAGACCATC 60.450 63.158 0.00 0.00 39.03 3.51
1522 1792 1.153628 GTGGAATCCTCCGACACCG 60.154 63.158 0.00 0.00 45.85 4.94
1563 1833 1.225704 CCAGGACAAGGAGGGCATC 59.774 63.158 0.00 0.00 0.00 3.91
1590 1860 2.178890 CCAGCAGCGCCTCATCTTC 61.179 63.158 2.29 0.00 0.00 2.87
1615 1885 2.663075 AAGCAGCTCGAGGATGGCA 61.663 57.895 15.58 0.00 0.00 4.92
1617 1887 2.108566 CAGCTCGAGGATGGCAGG 59.891 66.667 15.58 0.00 0.00 4.85
1731 2459 2.229792 GGCAAGACCATCACACTTGAA 58.770 47.619 0.00 0.00 42.12 2.69
1955 2911 2.208431 CTGCTGCTATTAGTCCTGTGC 58.792 52.381 0.00 0.00 0.00 4.57
1991 2947 9.303537 GTTAAGTCTACTGTATCTGGTTTGATC 57.696 37.037 0.00 0.00 0.00 2.92
1999 2955 4.405680 TGTATCTGGTTTGATCGACCATCT 59.594 41.667 18.00 12.06 45.56 2.90
2063 3019 7.255139 GCTGGTATGGTTTGGTATGAATAAGTC 60.255 40.741 0.00 0.00 0.00 3.01
2086 3042 9.807649 AGTCAATTTGAACCAATATGCTTATTC 57.192 29.630 0.00 0.00 0.00 1.75
2122 3078 6.604396 TGATTTGATATCTGCTGGTTGAATGT 59.396 34.615 3.98 0.00 0.00 2.71
2158 3122 8.726870 TTTTACAACTAGCAGTGATATTACCC 57.273 34.615 0.00 0.00 0.00 3.69
2312 3279 1.552337 TCTGCTTGCTTGCTACTAGCT 59.448 47.619 9.49 0.00 42.97 3.32
2368 3335 1.975680 GTGGGGTGTCTTCAGTAAGGA 59.024 52.381 0.00 0.00 33.22 3.36
2393 3360 3.389925 AAATGCATGAAGTTGTGGTGG 57.610 42.857 0.00 0.00 0.00 4.61
2581 4153 0.877743 GCCTGAGTGCAAGGACTTTC 59.122 55.000 7.13 0.00 0.00 2.62
2586 4158 1.265365 GAGTGCAAGGACTTTCACTGC 59.735 52.381 19.30 9.30 39.60 4.40
2604 4176 3.749609 ACTGCCCGAATTACTTGTGTTAC 59.250 43.478 0.00 0.00 0.00 2.50
2605 4177 4.000988 CTGCCCGAATTACTTGTGTTACT 58.999 43.478 0.00 0.00 0.00 2.24
2625 4245 3.071312 ACTGATGCATCTTCTCATCTCCC 59.929 47.826 26.32 0.00 39.69 4.30
2631 4251 3.493002 GCATCTTCTCATCTCCCTGTCTG 60.493 52.174 0.00 0.00 0.00 3.51
2685 4311 8.823220 ATGTTTTGTATGCTTATTACTCCCTT 57.177 30.769 0.00 0.00 0.00 3.95
2690 4316 9.742144 TTTGTATGCTTATTACTCCCTTTGTAA 57.258 29.630 0.00 0.00 34.87 2.41
2691 4317 9.742144 TTGTATGCTTATTACTCCCTTTGTAAA 57.258 29.630 0.00 0.00 34.20 2.01
2692 4318 9.169592 TGTATGCTTATTACTCCCTTTGTAAAC 57.830 33.333 0.00 0.00 34.20 2.01
2693 4319 9.392259 GTATGCTTATTACTCCCTTTGTAAACT 57.608 33.333 0.00 0.00 34.20 2.66
2696 4322 9.969001 TGCTTATTACTCCCTTTGTAAACTAAT 57.031 29.630 0.00 0.00 34.20 1.73
2736 4362 9.250624 GATCACTACTTTAATGATCTAAACGCT 57.749 33.333 8.21 0.00 43.55 5.07
2737 4363 8.630278 TCACTACTTTAATGATCTAAACGCTC 57.370 34.615 0.00 0.00 0.00 5.03
2738 4364 8.467598 TCACTACTTTAATGATCTAAACGCTCT 58.532 33.333 0.00 0.00 0.00 4.09
2739 4365 9.088512 CACTACTTTAATGATCTAAACGCTCTT 57.911 33.333 0.00 0.00 0.00 2.85
2756 4382 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2757 4383 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2758 4384 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2759 4385 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2760 4386 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2825 4451 4.626287 GCAACCACTTATCCTTCAGATGGA 60.626 45.833 7.49 7.49 36.33 3.41
2828 4454 4.163078 ACCACTTATCCTTCAGATGGACTG 59.837 45.833 7.20 3.94 46.97 3.51
2848 4474 6.350780 GGACTGCAGGAAATTCTTCATTCATT 60.351 38.462 19.93 0.00 32.75 2.57
2849 4475 6.628185 ACTGCAGGAAATTCTTCATTCATTC 58.372 36.000 19.93 0.00 32.75 2.67
2863 4489 1.275666 TCATTCCTCCTCCGAGCAAA 58.724 50.000 0.00 0.00 34.49 3.68
2882 4508 7.383300 CGAGCAAAGATTTTCATTTTCCTTTCT 59.617 33.333 0.00 0.00 0.00 2.52
2884 4510 7.989170 AGCAAAGATTTTCATTTTCCTTTCTGT 59.011 29.630 0.00 0.00 0.00 3.41
2885 4511 9.260002 GCAAAGATTTTCATTTTCCTTTCTGTA 57.740 29.630 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 102 0.249073 CGACGAGCCTAGGGTTGATG 60.249 60.000 30.94 19.21 0.00 3.07
198 212 5.783875 ACTAAAACTCCTAGGCTCCAACTAA 59.216 40.000 2.96 0.00 0.00 2.24
211 225 0.034337 TCGGCGCAACTAAAACTCCT 59.966 50.000 10.83 0.00 0.00 3.69
306 357 0.935196 GTCCACGCGAAATCCATACC 59.065 55.000 15.93 0.00 0.00 2.73
355 406 8.499162 CGAACAGATATAGCCCTTCAATAAAAG 58.501 37.037 0.00 0.00 0.00 2.27
369 424 8.425577 AATTCAACCAAGACGAACAGATATAG 57.574 34.615 0.00 0.00 0.00 1.31
372 427 5.642063 GGAATTCAACCAAGACGAACAGATA 59.358 40.000 7.93 0.00 0.00 1.98
398 453 4.348863 ACATCTGAGACCATAAGCCATC 57.651 45.455 0.00 0.00 0.00 3.51
423 481 8.992073 CATACTAGCAGATAAAACATGCATACA 58.008 33.333 0.00 0.00 42.45 2.29
424 482 7.959651 GCATACTAGCAGATAAAACATGCATAC 59.040 37.037 0.00 0.00 42.45 2.39
448 510 0.323629 AATTCGAGAAGGAACGGGCA 59.676 50.000 0.00 0.00 0.00 5.36
572 781 6.266786 TCGGACATGCTTACCATCTAATCTAA 59.733 38.462 0.00 0.00 29.71 2.10
573 782 5.773176 TCGGACATGCTTACCATCTAATCTA 59.227 40.000 0.00 0.00 29.71 1.98
574 783 4.588951 TCGGACATGCTTACCATCTAATCT 59.411 41.667 0.00 0.00 29.71 2.40
575 784 4.686554 GTCGGACATGCTTACCATCTAATC 59.313 45.833 2.62 0.00 29.71 1.75
576 785 4.100963 TGTCGGACATGCTTACCATCTAAT 59.899 41.667 6.76 0.00 29.71 1.73
626 835 6.268566 ACGACAGGTTAAAATCTACCGATAC 58.731 40.000 0.00 0.00 39.46 2.24
631 840 5.476614 ACAGACGACAGGTTAAAATCTACC 58.523 41.667 0.00 0.00 34.54 3.18
686 915 1.131693 GCGAGAATAAACAAACGGGGG 59.868 52.381 0.00 0.00 0.00 5.40
687 916 1.131693 GGCGAGAATAAACAAACGGGG 59.868 52.381 0.00 0.00 0.00 5.73
688 917 2.081462 AGGCGAGAATAAACAAACGGG 58.919 47.619 0.00 0.00 0.00 5.28
706 935 2.950781 TCTAGATGTGCCCTAGACAGG 58.049 52.381 0.00 0.00 38.08 4.00
750 979 8.792633 CCTTTTTATGTTTGATGGAGTCACTTA 58.207 33.333 0.00 0.00 36.32 2.24
751 980 7.505585 TCCTTTTTATGTTTGATGGAGTCACTT 59.494 33.333 0.00 0.00 36.32 3.16
752 981 7.004086 TCCTTTTTATGTTTGATGGAGTCACT 58.996 34.615 0.00 0.00 36.32 3.41
784 1021 5.354234 TCATGCGGGTAATCTTCTTCTTTTC 59.646 40.000 0.00 0.00 0.00 2.29
787 1024 4.487714 TCATGCGGGTAATCTTCTTCTT 57.512 40.909 0.00 0.00 0.00 2.52
788 1025 4.192317 GTTCATGCGGGTAATCTTCTTCT 58.808 43.478 0.00 0.00 0.00 2.85
789 1026 3.312697 GGTTCATGCGGGTAATCTTCTTC 59.687 47.826 0.00 0.00 0.00 2.87
860 1098 6.811170 GCTAAAGCACATCTAGGTCAGATATC 59.189 42.308 0.00 0.00 40.52 1.63
930 1168 7.596248 ACAGCAAGCAAAGTAACATGATAAAAG 59.404 33.333 0.00 0.00 0.00 2.27
932 1170 6.862608 CACAGCAAGCAAAGTAACATGATAAA 59.137 34.615 0.00 0.00 0.00 1.40
1074 1344 0.745845 CCTGGATCTTGGCCTTGACG 60.746 60.000 3.32 0.00 0.00 4.35
1221 1491 1.220169 CGAAGATCTGCATGCCTCCG 61.220 60.000 16.68 0.00 0.00 4.63
1305 1575 2.496899 TGTCCTGAATCTTGGCCTTC 57.503 50.000 3.32 0.00 0.00 3.46
1317 1587 1.274703 GGATGCCCTCCTTGTCCTGA 61.275 60.000 0.00 0.00 41.29 3.86
1425 1695 1.671742 GCGGAGGACAAGGTGAAGA 59.328 57.895 0.00 0.00 0.00 2.87
1449 1719 0.883814 CGAAGATCTGCATGCCTCCC 60.884 60.000 16.68 2.05 0.00 4.30
1470 1740 1.672356 CTTGCCGGTGAGGGTCTTG 60.672 63.158 1.90 0.00 41.48 3.02
1482 1752 0.518636 CAAGTGTGATGGTCTTGCCG 59.481 55.000 0.00 0.00 41.21 5.69
1494 1764 2.867109 AGGATTCCACCTCAAGTGTG 57.133 50.000 5.29 0.00 45.74 3.82
1522 1792 1.155424 TTGGCCTTCACGTTGTCGAC 61.155 55.000 9.11 9.11 40.62 4.20
1533 1803 0.620556 TGTCCTGGATCTTGGCCTTC 59.379 55.000 3.32 0.00 0.00 3.46
1605 1875 2.370445 AAGGGTCCTGCCATCCTCG 61.370 63.158 0.00 0.00 39.65 4.63
1615 1885 1.348036 GTTGTAGTCAGCAAGGGTCCT 59.652 52.381 0.00 0.00 0.00 3.85
1617 1887 2.543777 TGTTGTAGTCAGCAAGGGTC 57.456 50.000 0.00 0.00 32.20 4.46
1731 2459 0.544357 TGGTGTCGGAGGATTCCACT 60.544 55.000 5.29 0.00 44.26 4.00
1955 2911 5.287226 ACAGTAGACTTAACACGAACAAGG 58.713 41.667 0.00 0.00 0.00 3.61
1991 2947 3.571828 ACATCATCAGGACTAGATGGTCG 59.428 47.826 0.00 0.00 42.38 4.79
1999 2955 3.582647 ACCAACACACATCATCAGGACTA 59.417 43.478 0.00 0.00 0.00 2.59
2110 3066 3.905784 CTGGAAGAAACATTCAACCAGC 58.094 45.455 16.42 0.00 42.97 4.85
2112 3068 5.930837 AAACTGGAAGAAACATTCAACCA 57.069 34.783 0.00 0.00 37.43 3.67
2122 3078 7.338449 ACTGCTAGTTGTAAAAACTGGAAGAAA 59.662 33.333 14.47 0.00 36.75 2.52
2158 3122 2.975732 TGCAATCAGAGAGCCACTAG 57.024 50.000 0.00 0.00 0.00 2.57
2225 3191 8.854614 AGAAGAAACATGGATATATAACTGGC 57.145 34.615 0.00 0.00 0.00 4.85
2312 3279 2.224281 ACGAGCAAAGACACTCCAATCA 60.224 45.455 0.00 0.00 0.00 2.57
2393 3360 6.374613 ACGAATTTTTCCTAAGGAATCCAGTC 59.625 38.462 0.61 0.00 41.71 3.51
2489 4061 8.266392 AGCAGAAGATTTTAGAGAACAGAATG 57.734 34.615 0.00 0.00 46.00 2.67
2581 4153 2.151202 ACACAAGTAATTCGGGCAGTG 58.849 47.619 0.00 0.00 0.00 3.66
2586 4158 5.447279 GCATCAGTAACACAAGTAATTCGGG 60.447 44.000 0.00 0.00 0.00 5.14
2604 4176 3.325425 AGGGAGATGAGAAGATGCATCAG 59.675 47.826 27.81 0.00 42.52 2.90
2605 4177 3.071167 CAGGGAGATGAGAAGATGCATCA 59.929 47.826 27.81 9.53 42.52 3.07
2625 4245 0.898320 AGAATCGTCCCCACAGACAG 59.102 55.000 0.00 0.00 36.52 3.51
2631 4251 1.271163 TGGAAACAGAATCGTCCCCAC 60.271 52.381 0.00 0.00 35.01 4.61
2710 4336 9.250624 AGCGTTTAGATCATTAAAGTAGTGATC 57.749 33.333 10.99 10.99 46.33 2.92
2711 4337 9.250624 GAGCGTTTAGATCATTAAAGTAGTGAT 57.749 33.333 0.00 0.00 37.77 3.06
2712 4338 8.467598 AGAGCGTTTAGATCATTAAAGTAGTGA 58.532 33.333 0.00 0.00 37.82 3.41
2713 4339 8.635877 AGAGCGTTTAGATCATTAAAGTAGTG 57.364 34.615 0.00 0.00 37.82 2.74
2730 4356 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2731 4357 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2732 4358 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2733 4359 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2734 4360 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2742 4368 9.577222 GAGATAGTACTCCCTCTGTAAACTAAT 57.423 37.037 0.00 0.00 0.00 1.73
2743 4369 8.780003 AGAGATAGTACTCCCTCTGTAAACTAA 58.220 37.037 20.03 0.00 37.60 2.24
2744 4370 8.334522 AGAGATAGTACTCCCTCTGTAAACTA 57.665 38.462 20.03 0.00 37.60 2.24
2745 4371 7.215743 AGAGATAGTACTCCCTCTGTAAACT 57.784 40.000 20.03 4.98 37.60 2.66
2746 4372 7.339976 ACAAGAGATAGTACTCCCTCTGTAAAC 59.660 40.741 20.92 3.83 36.26 2.01
2747 4373 7.339721 CACAAGAGATAGTACTCCCTCTGTAAA 59.660 40.741 20.92 0.00 36.26 2.01
2748 4374 6.829298 CACAAGAGATAGTACTCCCTCTGTAA 59.171 42.308 20.92 0.00 36.26 2.41
2749 4375 6.069556 ACACAAGAGATAGTACTCCCTCTGTA 60.070 42.308 20.92 0.00 36.26 2.74
2750 4376 5.197451 CACAAGAGATAGTACTCCCTCTGT 58.803 45.833 20.92 17.84 36.26 3.41
2751 4377 5.197451 ACACAAGAGATAGTACTCCCTCTG 58.803 45.833 20.92 17.41 36.26 3.35
2752 4378 5.459982 ACACAAGAGATAGTACTCCCTCT 57.540 43.478 16.79 16.79 37.58 3.69
2753 4379 5.163499 CCAACACAAGAGATAGTACTCCCTC 60.163 48.000 13.63 13.63 37.60 4.30
2754 4380 4.712337 CCAACACAAGAGATAGTACTCCCT 59.288 45.833 0.00 0.00 37.60 4.20
2755 4381 4.710375 TCCAACACAAGAGATAGTACTCCC 59.290 45.833 0.00 0.00 37.60 4.30
2756 4382 5.163499 CCTCCAACACAAGAGATAGTACTCC 60.163 48.000 0.00 0.00 37.60 3.85
2757 4383 5.419471 ACCTCCAACACAAGAGATAGTACTC 59.581 44.000 0.00 0.00 37.19 2.59
2758 4384 5.186021 CACCTCCAACACAAGAGATAGTACT 59.814 44.000 0.00 0.00 31.43 2.73
2759 4385 5.185249 TCACCTCCAACACAAGAGATAGTAC 59.815 44.000 0.00 0.00 31.43 2.73
2760 4386 5.185249 GTCACCTCCAACACAAGAGATAGTA 59.815 44.000 0.00 0.00 31.43 1.82
2761 4387 4.021016 GTCACCTCCAACACAAGAGATAGT 60.021 45.833 0.00 0.00 31.43 2.12
2762 4388 4.221703 AGTCACCTCCAACACAAGAGATAG 59.778 45.833 0.00 0.00 31.43 2.08
2763 4389 4.021104 CAGTCACCTCCAACACAAGAGATA 60.021 45.833 0.00 0.00 31.43 1.98
2764 4390 2.975489 AGTCACCTCCAACACAAGAGAT 59.025 45.455 0.00 0.00 31.43 2.75
2765 4391 2.103094 CAGTCACCTCCAACACAAGAGA 59.897 50.000 0.00 0.00 31.43 3.10
2766 4392 2.103094 TCAGTCACCTCCAACACAAGAG 59.897 50.000 0.00 0.00 0.00 2.85
2767 4393 2.115427 TCAGTCACCTCCAACACAAGA 58.885 47.619 0.00 0.00 0.00 3.02
2825 4451 6.350780 GGAATGAATGAAGAATTTCCTGCAGT 60.351 38.462 13.81 0.00 32.09 4.40
2828 4454 6.218108 AGGAATGAATGAAGAATTTCCTGC 57.782 37.500 1.41 0.00 33.51 4.85
2848 4474 1.573108 AATCTTTGCTCGGAGGAGGA 58.427 50.000 7.20 6.90 40.80 3.71
2849 4475 2.409948 AAATCTTTGCTCGGAGGAGG 57.590 50.000 7.20 1.50 40.80 4.30
2863 4489 9.799106 TCTCTACAGAAAGGAAAATGAAAATCT 57.201 29.630 0.00 0.00 0.00 2.40
2882 4508 5.516059 TTGTAGAACCTCCTCTCTCTACA 57.484 43.478 6.68 6.68 45.23 2.74
2884 4510 9.543231 TTTAATTTGTAGAACCTCCTCTCTCTA 57.457 33.333 0.00 0.00 0.00 2.43
2885 4511 8.437274 TTTAATTTGTAGAACCTCCTCTCTCT 57.563 34.615 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.