Multiple sequence alignment - TraesCS6B01G196100

Loading Multiple Alignment...

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 TraesCS6B01G196100 chr6B 100.000 4567 0 0 1 4567 232322698 232327264 0.000000e+00 8434.0
1 TraesCS6B01G196100 chr6B 81.831 710 77 32 1025 1699 232590043 232590735 2.400000e-152 549.0
2 TraesCS6B01G196100 chr6B 76.995 1065 177 45 3291 4333 232591906 232592924 8.640000e-152 547.0
3 TraesCS6B01G196100 chr6B 97.674 86 1 1 2640 2724 225523365 225523450 3.680000e-31 147.0
4 TraesCS6B01G196100 chr6B 80.095 211 27 12 1 201 693072640 693072435 4.760000e-30 143.0
5 TraesCS6B01G196100 chr6D 92.209 1874 93 25 2722 4567 133482350 133484198 0.000000e+00 2603.0
6 TraesCS6B01G196100 chr6D 94.031 1022 34 9 893 1906 133480454 133481456 0.000000e+00 1524.0
7 TraesCS6B01G196100 chr6D 93.848 959 36 10 1 950 133479513 133480457 0.000000e+00 1423.0
8 TraesCS6B01G196100 chr6D 89.820 668 31 20 2004 2641 133481691 133482351 0.000000e+00 822.0
9 TraesCS6B01G196100 chr6D 77.911 1168 148 62 605 1699 133580941 133582071 1.080000e-175 627.0
10 TraesCS6B01G196100 chr6D 77.997 1168 141 64 605 1699 133954614 133955738 1.080000e-175 627.0
11 TraesCS6B01G196100 chr6D 81.702 705 86 22 1025 1699 133882768 133883459 8.640000e-152 547.0
12 TraesCS6B01G196100 chr6D 76.476 1016 161 47 3291 4278 133583241 133584206 8.890000e-132 481.0
13 TraesCS6B01G196100 chr6D 75.820 1067 180 51 3291 4332 133956906 133957919 1.920000e-128 470.0
14 TraesCS6B01G196100 chr6D 76.209 1013 166 48 3291 4278 133884621 133885583 2.490000e-127 466.0
15 TraesCS6B01G196100 chr6D 88.462 104 8 3 2639 2738 382350247 382350144 6.200000e-24 122.0
16 TraesCS6B01G196100 chr6A 91.934 1810 103 23 2722 4504 173435386 173437179 0.000000e+00 2494.0
17 TraesCS6B01G196100 chr6A 90.444 1800 125 23 2790 4567 173122967 173124741 0.000000e+00 2327.0
18 TraesCS6B01G196100 chr6A 92.318 1536 59 20 893 2402 173433593 173435095 0.000000e+00 2128.0
19 TraesCS6B01G196100 chr6A 91.847 1435 80 13 893 2313 173113932 173115343 0.000000e+00 1967.0
20 TraesCS6B01G196100 chr6A 92.395 881 40 13 72 950 173432741 173433596 0.000000e+00 1230.0
21 TraesCS6B01G196100 chr6A 94.315 387 12 5 1 384 173113337 173113716 6.580000e-163 584.0
22 TraesCS6B01G196100 chr6A 76.909 1100 157 56 668 1699 174449377 174450447 6.730000e-148 534.0
23 TraesCS6B01G196100 chr6A 78.558 513 95 11 1032 1543 173315238 173315736 1.580000e-84 324.0
24 TraesCS6B01G196100 chr6A 93.213 221 10 3 730 950 173113720 173113935 2.050000e-83 320.0
25 TraesCS6B01G196100 chr6A 91.304 184 11 4 2461 2641 173435206 173435387 3.530000e-61 246.0
26 TraesCS6B01G196100 chr6A 95.349 86 3 1 2640 2724 169203395 169203310 7.970000e-28 135.0
27 TraesCS6B01G196100 chr6A 78.733 221 30 14 1 209 602635501 602635286 1.030000e-26 132.0
28 TraesCS6B01G196100 chr6A 95.833 48 2 0 2722 2769 173122923 173122970 1.360000e-10 78.7
29 TraesCS6B01G196100 chr2D 74.855 517 83 26 3315 3809 593114903 593115394 1.680000e-44 191.0
30 TraesCS6B01G196100 chr2A 74.427 524 95 21 3315 3809 727444609 727445122 6.030000e-44 189.0
31 TraesCS6B01G196100 chr2A 73.905 525 101 22 3315 3809 727392314 727392832 1.310000e-40 178.0
32 TraesCS6B01G196100 chr2A 93.684 95 4 2 2640 2732 404608293 404608199 1.710000e-29 141.0
33 TraesCS6B01G196100 chr2A 89.899 99 8 2 2640 2736 158043305 158043403 4.800000e-25 126.0
34 TraesCS6B01G196100 chrUn 79.911 224 33 11 1 216 112250670 112250889 2.200000e-33 154.0
35 TraesCS6B01G196100 chr1A 94.505 91 3 2 2640 2728 477033463 477033553 6.160000e-29 139.0
36 TraesCS6B01G196100 chr1A 94.444 90 3 2 2640 2727 435389824 435389913 2.220000e-28 137.0
37 TraesCS6B01G196100 chr5A 93.548 93 4 1 2639 2729 670269928 670270020 2.220000e-28 137.0
38 TraesCS6B01G196100 chr7B 95.294 85 3 1 2640 2723 131183318 131183234 2.870000e-27 134.0
39 TraesCS6B01G196100 chr3A 79.851 134 15 7 4 133 465544529 465544404 2.260000e-13 87.9
40 TraesCS6B01G196100 chr3D 89.062 64 5 2 1 63 339250394 339250456 1.360000e-10 78.7


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 TraesCS6B01G196100 chr6B 232322698 232327264 4566 False 8434.00 8434 100.00000 1 4567 1 chr6B.!!$F2 4566
1 TraesCS6B01G196100 chr6B 232590043 232592924 2881 False 548.00 549 79.41300 1025 4333 2 chr6B.!!$F3 3308
2 TraesCS6B01G196100 chr6D 133479513 133484198 4685 False 1593.00 2603 92.47700 1 4567 4 chr6D.!!$F1 4566
3 TraesCS6B01G196100 chr6D 133580941 133584206 3265 False 554.00 627 77.19350 605 4278 2 chr6D.!!$F2 3673
4 TraesCS6B01G196100 chr6D 133954614 133957919 3305 False 548.50 627 76.90850 605 4332 2 chr6D.!!$F4 3727
5 TraesCS6B01G196100 chr6D 133882768 133885583 2815 False 506.50 547 78.95550 1025 4278 2 chr6D.!!$F3 3253
6 TraesCS6B01G196100 chr6A 173432741 173437179 4438 False 1524.50 2494 91.98775 72 4504 4 chr6A.!!$F5 4432
7 TraesCS6B01G196100 chr6A 173122923 173124741 1818 False 1202.85 2327 93.13850 2722 4567 2 chr6A.!!$F4 1845
8 TraesCS6B01G196100 chr6A 173113337 173115343 2006 False 957.00 1967 93.12500 1 2313 3 chr6A.!!$F3 2312
9 TraesCS6B01G196100 chr6A 174449377 174450447 1070 False 534.00 534 76.90900 668 1699 1 chr6A.!!$F2 1031

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
495 507 0.028902 AAACTGCGCGAAACAAGACC 59.971 50.0 12.10 0.00 0.00 3.85 F
1746 2115 0.538057 TACTAGTGGATACGGCCGGG 60.538 60.0 31.76 2.28 42.51 5.73 F
2198 2773 0.963355 AGAGGTCACGTCAGAGAGGC 60.963 60.0 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2964 0.178068 ACATCTACACCGATGCACCC 59.822 55.000 0.00 0.0 43.54 4.61 R
2604 3254 0.678048 GCCGAGGCTTGATGTCCTTT 60.678 55.000 6.90 0.0 38.26 3.11 R
3796 4587 1.496001 ACCATGGCAATAGAGCATCCA 59.504 47.619 13.04 0.0 33.66 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
406 418 3.478857 TTTCCGTGTTTTAGCTCCTGA 57.521 42.857 0.00 0.00 0.00 3.86
483 495 1.946768 TCTCCCTTCAACAAAACTGCG 59.053 47.619 0.00 0.00 0.00 5.18
495 507 0.028902 AAACTGCGCGAAACAAGACC 59.971 50.000 12.10 0.00 0.00 3.85
661 674 8.611654 AGGCAAAAACGAAAATAAGAGTAGTA 57.388 30.769 0.00 0.00 0.00 1.82
727 740 5.450550 GGAAAGAAACACTTGAAACCCTCTG 60.451 44.000 0.00 0.00 38.98 3.35
732 745 3.041946 ACACTTGAAACCCTCTGTCTCT 58.958 45.455 0.00 0.00 0.00 3.10
775 788 0.845102 TCTCCCCTTTCCTCCCAACC 60.845 60.000 0.00 0.00 0.00 3.77
787 800 9.502035 CCTTTCCTCCCAACCACTATATATATA 57.498 37.037 2.49 2.49 0.00 0.86
883 915 1.195115 TCCAGGTAGCACAGATGTCC 58.805 55.000 0.00 0.00 0.00 4.02
891 923 1.761784 AGCACAGATGTCCATCTCTCC 59.238 52.381 6.82 0.00 45.78 3.71
965 1057 1.818060 TGTTTTGCTTGTGTCTGCTGT 59.182 42.857 0.00 0.00 0.00 4.40
966 1058 2.159393 TGTTTTGCTTGTGTCTGCTGTC 60.159 45.455 0.00 0.00 0.00 3.51
967 1059 1.748950 TTTGCTTGTGTCTGCTGTCA 58.251 45.000 0.00 0.00 0.00 3.58
968 1060 1.748950 TTGCTTGTGTCTGCTGTCAA 58.251 45.000 0.00 0.00 0.00 3.18
1020 1112 4.120331 GGCATGCTGTTCGGCCAC 62.120 66.667 18.92 0.00 45.70 5.01
1023 1127 2.115052 ATGCTGTTCGGCCACCAA 59.885 55.556 2.24 0.00 0.00 3.67
1619 1781 4.719773 ACCACATGGCTAAATACTGGAGTA 59.280 41.667 0.00 0.00 39.32 2.59
1620 1782 5.369699 ACCACATGGCTAAATACTGGAGTAT 59.630 40.000 0.00 0.00 39.79 2.12
1621 1783 5.934625 CCACATGGCTAAATACTGGAGTATC 59.065 44.000 0.00 0.00 40.10 2.24
1681 1847 4.460382 ACAAGATCCGACGTTAGAAGGTAA 59.540 41.667 0.00 0.00 0.00 2.85
1746 2115 0.538057 TACTAGTGGATACGGCCGGG 60.538 60.000 31.76 2.28 42.51 5.73
2044 2619 1.343465 CGTCATACCCTGTACATCCCC 59.657 57.143 0.00 0.00 0.00 4.81
2081 2656 1.260561 CGCGGCTAATGGTGTCATTAC 59.739 52.381 0.00 0.00 42.90 1.89
2191 2766 2.916052 GCCGACAGAGGTCACGTCA 61.916 63.158 0.00 0.00 44.54 4.35
2198 2773 0.963355 AGAGGTCACGTCAGAGAGGC 60.963 60.000 0.00 0.00 0.00 4.70
2208 2783 3.063084 AGAGAGGCCCGTCACGTC 61.063 66.667 0.00 0.00 0.00 4.34
2259 2838 2.828549 GGTGCTAACCATGGGCGG 60.829 66.667 18.09 6.22 46.75 6.13
2319 2905 1.130561 GCCAAGTCGCCAAGTCATTAC 59.869 52.381 0.00 0.00 0.00 1.89
2335 2921 7.765695 AGTCATTACCATTTGAAACATCACT 57.234 32.000 0.00 0.00 0.00 3.41
2336 2922 8.181904 AGTCATTACCATTTGAAACATCACTT 57.818 30.769 0.00 0.00 0.00 3.16
2376 2964 4.065789 CTCATCATGGATGTGAGTGATGG 58.934 47.826 12.59 2.68 44.91 3.51
2416 3035 8.562892 AGATGTCTGTTGAGTAAAATGTGAAAG 58.437 33.333 0.00 0.00 0.00 2.62
2440 3059 7.788026 AGGAATTGTGATACCACGAGTAATAA 58.212 34.615 0.00 0.00 46.06 1.40
2441 3060 8.429641 AGGAATTGTGATACCACGAGTAATAAT 58.570 33.333 0.00 0.00 46.06 1.28
2442 3061 9.701098 GGAATTGTGATACCACGAGTAATAATA 57.299 33.333 0.00 0.00 46.06 0.98
2506 3151 3.193263 CGGATGCAGAGCCATATATCAC 58.807 50.000 0.00 0.00 0.00 3.06
2556 3206 7.990314 TCAATCTTTTTCCCGTGATGTATATCA 59.010 33.333 0.00 0.00 40.92 2.15
2557 3207 8.786898 CAATCTTTTTCCCGTGATGTATATCAT 58.213 33.333 5.38 0.00 44.62 2.45
2641 3291 3.040409 CGAAGCGGTACAACCCTAC 57.960 57.895 0.00 0.00 33.75 3.18
2642 3292 0.529378 CGAAGCGGTACAACCCTACT 59.471 55.000 0.00 0.00 33.75 2.57
2643 3293 1.468736 CGAAGCGGTACAACCCTACTC 60.469 57.143 0.00 0.00 33.75 2.59
2644 3294 0.900421 AAGCGGTACAACCCTACTCC 59.100 55.000 0.00 0.00 33.75 3.85
2645 3295 0.974525 AGCGGTACAACCCTACTCCC 60.975 60.000 0.00 0.00 33.75 4.30
2646 3296 0.974525 GCGGTACAACCCTACTCCCT 60.975 60.000 0.00 0.00 33.75 4.20
2647 3297 1.109609 CGGTACAACCCTACTCCCTC 58.890 60.000 0.00 0.00 33.75 4.30
2648 3298 1.493861 GGTACAACCCTACTCCCTCC 58.506 60.000 0.00 0.00 30.04 4.30
2649 3299 1.109609 GTACAACCCTACTCCCTCCG 58.890 60.000 0.00 0.00 0.00 4.63
2650 3300 0.706433 TACAACCCTACTCCCTCCGT 59.294 55.000 0.00 0.00 0.00 4.69
2651 3301 0.614134 ACAACCCTACTCCCTCCGTC 60.614 60.000 0.00 0.00 0.00 4.79
2652 3302 0.324460 CAACCCTACTCCCTCCGTCT 60.324 60.000 0.00 0.00 0.00 4.18
2653 3303 0.033306 AACCCTACTCCCTCCGTCTC 60.033 60.000 0.00 0.00 0.00 3.36
2654 3304 1.212934 ACCCTACTCCCTCCGTCTCA 61.213 60.000 0.00 0.00 0.00 3.27
2655 3305 0.186386 CCCTACTCCCTCCGTCTCAT 59.814 60.000 0.00 0.00 0.00 2.90
2656 3306 1.424302 CCCTACTCCCTCCGTCTCATA 59.576 57.143 0.00 0.00 0.00 2.15
2657 3307 2.158505 CCCTACTCCCTCCGTCTCATAA 60.159 54.545 0.00 0.00 0.00 1.90
2658 3308 3.500654 CCCTACTCCCTCCGTCTCATAAT 60.501 52.174 0.00 0.00 0.00 1.28
2659 3309 3.508012 CCTACTCCCTCCGTCTCATAATG 59.492 52.174 0.00 0.00 0.00 1.90
2660 3310 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
2661 3311 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
2662 3312 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
2663 3313 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
2664 3314 4.800023 TCCCTCCGTCTCATAATGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
2665 3315 4.583489 TCCCTCCGTCTCATAATGTAAGAC 59.417 45.833 0.00 0.00 36.82 3.01
2715 3365 7.989416 AAAAAGTCTTACATTATGGGACGAA 57.011 32.000 0.00 0.00 32.86 3.85
2716 3366 7.611213 AAAAGTCTTACATTATGGGACGAAG 57.389 36.000 0.00 0.00 32.86 3.79
2717 3367 5.277857 AGTCTTACATTATGGGACGAAGG 57.722 43.478 0.00 0.00 32.86 3.46
2718 3368 4.101119 AGTCTTACATTATGGGACGAAGGG 59.899 45.833 0.00 0.00 32.86 3.95
2719 3369 4.100498 GTCTTACATTATGGGACGAAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
2720 3370 4.344102 TCTTACATTATGGGACGAAGGGAG 59.656 45.833 0.00 0.00 0.00 4.30
2777 3427 3.566273 TGCATTTTCAACTGCACCG 57.434 47.368 0.71 0.00 43.11 4.94
2778 3428 0.031857 TGCATTTTCAACTGCACCGG 59.968 50.000 0.00 0.00 43.11 5.28
2825 3476 1.728971 GGCATTCGAGGATATCAAGCG 59.271 52.381 4.83 5.02 0.00 4.68
2950 3603 9.959749 AAAATTCATCAACTTTGTACGTGTTAT 57.040 25.926 0.00 0.00 0.00 1.89
2956 3609 9.051027 CATCAACTTTGTACGTGTTATTTCATC 57.949 33.333 0.00 0.00 0.00 2.92
2960 3613 7.803724 ACTTTGTACGTGTTATTTCATCCTTC 58.196 34.615 0.00 0.00 0.00 3.46
2983 3636 6.291377 TCTCTATGTGAAAAGACAGTGCTTT 58.709 36.000 6.70 6.70 39.65 3.51
2997 3650 2.304761 AGTGCTTTTATCGGTTCCTCCA 59.695 45.455 0.00 0.00 35.57 3.86
3004 3659 5.699097 TTTATCGGTTCCTCCACAAAAAG 57.301 39.130 0.00 0.00 35.57 2.27
3016 3671 7.629157 TCCTCCACAAAAAGGAAAAAGAAAAT 58.371 30.769 0.00 0.00 38.74 1.82
3129 3785 9.152595 CCTGGAGTAGTTTAGTTTTGTCTTATC 57.847 37.037 0.00 0.00 0.00 1.75
3130 3786 9.152595 CTGGAGTAGTTTAGTTTTGTCTTATCC 57.847 37.037 0.00 0.00 0.00 2.59
3611 4393 5.277825 TGTCACCAATTTCGACATTGTTTC 58.722 37.500 19.89 9.92 34.83 2.78
3679 4462 5.503634 TGTTGATCTTTTCCCTCTCATGA 57.496 39.130 0.00 0.00 0.00 3.07
3696 4480 7.202075 CCTCTCATGATCTAGAGATGGGAAAAA 60.202 40.741 14.92 0.00 41.51 1.94
3814 4605 2.578786 TGTGGATGCTCTATTGCCATG 58.421 47.619 0.00 0.00 0.00 3.66
3827 4618 5.827797 TCTATTGCCATGGTCTTGGTATTTC 59.172 40.000 14.67 0.00 39.11 2.17
3860 4651 9.823647 ATAATGGATCCTATGATATCGTGTTTC 57.176 33.333 14.23 0.18 0.00 2.78
3941 4733 9.906111 GTTCAAAGAAAAATTGAGCTTAGTTTG 57.094 29.630 0.00 0.00 38.01 2.93
3965 4761 2.999355 GAGTCAGAATTGTCCTGCAGTC 59.001 50.000 13.81 6.09 0.00 3.51
3989 4785 3.081409 CCCTCCCCACGTCCGATT 61.081 66.667 0.00 0.00 0.00 3.34
4001 4800 3.062042 ACGTCCGATTTCCAGTTTGTAC 58.938 45.455 0.00 0.00 0.00 2.90
4197 5007 8.390354 TCGACATTGAAATACTTGATGCTTTAG 58.610 33.333 0.00 0.00 0.00 1.85
4214 5051 7.572523 TGCTTTAGCTTATACGTAGGACTTA 57.427 36.000 0.08 0.00 42.66 2.24
4215 5052 7.646314 TGCTTTAGCTTATACGTAGGACTTAG 58.354 38.462 0.08 0.00 42.66 2.18
4216 5053 7.284034 TGCTTTAGCTTATACGTAGGACTTAGT 59.716 37.037 0.08 0.00 42.66 2.24
4220 5057 9.793252 TTAGCTTATACGTAGGACTTAGTTTTG 57.207 33.333 0.08 0.00 0.00 2.44
4221 5058 7.263496 AGCTTATACGTAGGACTTAGTTTTGG 58.737 38.462 0.08 0.00 0.00 3.28
4313 5169 7.061673 GTGCTCGAAGATGTGATAGTTGATATC 59.938 40.741 0.00 0.00 37.37 1.63
4367 5223 6.688073 TGGCCCAAAATAACATTTTAGGAA 57.312 33.333 11.47 0.00 0.00 3.36
4416 5275 8.392612 GTGATGTGACTCTAACTCTAGTAGTTC 58.607 40.741 9.83 0.00 45.64 3.01
4477 5337 9.974980 TCACAGTTCTTTAGTTTTTCTGTTTTT 57.025 25.926 0.00 0.00 33.35 1.94
4497 5357 8.632679 TGTTTTTGAAAAAGATAGCTCTCACAT 58.367 29.630 2.91 0.00 0.00 3.21
4540 5411 6.651225 GGAGCTGTCACAGTTCTTTAGTTAAT 59.349 38.462 19.84 0.00 40.65 1.40
4562 5433 5.943349 TGAAGGACATTCCGAAATAGGTA 57.057 39.130 0.00 0.00 42.75 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.518634 TTTGAGCACCTTTTGAACACC 57.481 42.857 0.00 0.00 0.00 4.16
214 225 9.440761 ACACCCTAATGGCCAATATAATAAAAA 57.559 29.630 10.96 0.00 37.83 1.94
216 227 9.747898 CTACACCCTAATGGCCAATATAATAAA 57.252 33.333 10.96 0.00 37.83 1.40
217 228 8.333235 CCTACACCCTAATGGCCAATATAATAA 58.667 37.037 10.96 0.00 37.83 1.40
220 231 5.852807 TCCTACACCCTAATGGCCAATATAA 59.147 40.000 10.96 0.00 37.83 0.98
351 363 8.762426 GTGAAGACGAAAACAAGACTAGTAATT 58.238 33.333 0.00 0.00 0.00 1.40
352 364 8.142551 AGTGAAGACGAAAACAAGACTAGTAAT 58.857 33.333 0.00 0.00 0.00 1.89
353 365 7.486647 AGTGAAGACGAAAACAAGACTAGTAA 58.513 34.615 0.00 0.00 0.00 2.24
354 366 7.035840 AGTGAAGACGAAAACAAGACTAGTA 57.964 36.000 0.00 0.00 0.00 1.82
406 418 3.569701 ACATCCTCGTGCATGTTTCTTTT 59.430 39.130 5.68 0.00 28.27 2.27
483 495 2.210116 TCTTCACTGGTCTTGTTTCGC 58.790 47.619 0.00 0.00 0.00 4.70
495 507 6.146837 CACTAGTCTTGTTTCCATCTTCACTG 59.853 42.308 0.00 0.00 0.00 3.66
625 638 3.442273 TCGTTTTTGCCTAGCTATTTGGG 59.558 43.478 0.00 0.00 0.00 4.12
661 674 3.506844 GGAGGAGTACGTCTTCAGTCTTT 59.493 47.826 0.00 0.00 32.77 2.52
727 740 5.506686 AAAGGAAAGAAAAGCACAGAGAC 57.493 39.130 0.00 0.00 0.00 3.36
732 745 5.046663 AGGTTCAAAAGGAAAGAAAAGCACA 60.047 36.000 0.00 0.00 37.23 4.57
883 915 6.293081 CGTTGGCATGTATAAAAGGAGAGATG 60.293 42.308 0.00 0.00 0.00 2.90
887 919 5.092554 TCGTTGGCATGTATAAAAGGAGA 57.907 39.130 0.00 0.00 0.00 3.71
891 923 6.347725 GCTAGGATCGTTGGCATGTATAAAAG 60.348 42.308 0.00 0.00 0.00 2.27
965 1057 4.610333 TGCTCTCTGTTCCTATACCTTGA 58.390 43.478 0.00 0.00 0.00 3.02
966 1058 5.112686 GTTGCTCTCTGTTCCTATACCTTG 58.887 45.833 0.00 0.00 0.00 3.61
967 1059 4.142138 CGTTGCTCTCTGTTCCTATACCTT 60.142 45.833 0.00 0.00 0.00 3.50
968 1060 3.381908 CGTTGCTCTCTGTTCCTATACCT 59.618 47.826 0.00 0.00 0.00 3.08
1062 1166 1.667830 CTTGAAGAACTCCGCGCCA 60.668 57.895 0.00 0.00 0.00 5.69
1092 1196 2.572104 GTTCTTGACCAGATAGGGGTGT 59.428 50.000 0.00 0.00 43.89 4.16
1276 1422 3.274586 CATCCATCCACAGCGCGG 61.275 66.667 8.83 5.83 0.00 6.46
1277 1423 3.945434 GCATCCATCCACAGCGCG 61.945 66.667 0.00 0.00 0.00 6.86
1278 1424 1.731433 ATTGCATCCATCCACAGCGC 61.731 55.000 0.00 0.00 0.00 5.92
1681 1847 5.284424 GCGAACGTTTCACAAAAAGTTTACT 59.716 36.000 0.46 0.00 43.88 2.24
1746 2115 2.141517 CCGTCAATCAGATCAGCATCC 58.858 52.381 0.00 0.00 0.00 3.51
1823 2204 4.608933 TCGCGTGCGAGCTAATAG 57.391 55.556 13.62 0.00 44.01 1.73
1989 2564 3.058160 GTGCTGCGGCTGTGGAAT 61.058 61.111 20.27 0.00 39.59 3.01
2044 2619 3.414700 GCGGTGGACGTGAAGCTG 61.415 66.667 0.00 0.00 46.52 4.24
2191 2766 3.063084 GACGTGACGGGCCTCTCT 61.063 66.667 10.66 0.00 0.00 3.10
2198 2773 4.778415 CTCCTGCGACGTGACGGG 62.778 72.222 10.66 0.00 0.00 5.28
2259 2838 4.179579 GCGCCGATCCACAAAGCC 62.180 66.667 0.00 0.00 0.00 4.35
2319 2905 7.278424 ACAAGACAAAAGTGATGTTTCAAATGG 59.722 33.333 0.00 0.00 32.48 3.16
2335 2921 3.214328 GAGGAGGCTTGACAAGACAAAA 58.786 45.455 22.99 0.00 39.74 2.44
2336 2922 2.172505 TGAGGAGGCTTGACAAGACAAA 59.827 45.455 22.99 0.76 39.74 2.83
2376 2964 0.178068 ACATCTACACCGATGCACCC 59.822 55.000 0.00 0.00 43.54 4.61
2396 2984 8.971321 CAATTCCTTTCACATTTTACTCAACAG 58.029 33.333 0.00 0.00 0.00 3.16
2416 3035 8.603242 ATTATTACTCGTGGTATCACAATTCC 57.397 34.615 6.97 0.00 43.79 3.01
2604 3254 0.678048 GCCGAGGCTTGATGTCCTTT 60.678 55.000 6.90 0.00 38.26 3.11
2637 3287 2.953284 TATGAGACGGAGGGAGTAGG 57.047 55.000 0.00 0.00 0.00 3.18
2639 3289 4.180377 ACATTATGAGACGGAGGGAGTA 57.820 45.455 0.00 0.00 0.00 2.59
2640 3290 3.033659 ACATTATGAGACGGAGGGAGT 57.966 47.619 0.00 0.00 0.00 3.85
2641 3291 4.827835 TCTTACATTATGAGACGGAGGGAG 59.172 45.833 0.00 0.00 0.00 4.30
2642 3292 4.583489 GTCTTACATTATGAGACGGAGGGA 59.417 45.833 0.00 0.00 34.53 4.20
2643 3293 4.872664 GTCTTACATTATGAGACGGAGGG 58.127 47.826 0.00 0.00 34.53 4.30
2691 3341 7.120726 CCTTCGTCCCATAATGTAAGACTTTTT 59.879 37.037 0.00 0.00 0.00 1.94
2692 3342 6.598064 CCTTCGTCCCATAATGTAAGACTTTT 59.402 38.462 0.00 0.00 0.00 2.27
2693 3343 6.113411 CCTTCGTCCCATAATGTAAGACTTT 58.887 40.000 0.00 0.00 0.00 2.66
2694 3344 5.396436 CCCTTCGTCCCATAATGTAAGACTT 60.396 44.000 0.00 0.00 0.00 3.01
2695 3345 4.101119 CCCTTCGTCCCATAATGTAAGACT 59.899 45.833 0.00 0.00 0.00 3.24
2696 3346 4.100498 TCCCTTCGTCCCATAATGTAAGAC 59.900 45.833 0.00 0.00 0.00 3.01
2697 3347 4.291792 TCCCTTCGTCCCATAATGTAAGA 58.708 43.478 0.00 0.00 0.00 2.10
2698 3348 4.101119 ACTCCCTTCGTCCCATAATGTAAG 59.899 45.833 0.00 0.00 0.00 2.34
2699 3349 4.035112 ACTCCCTTCGTCCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
2700 3350 3.649843 ACTCCCTTCGTCCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
2701 3351 2.478292 ACTCCCTTCGTCCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
2702 3352 4.891992 ATACTCCCTTCGTCCCATAATG 57.108 45.455 0.00 0.00 0.00 1.90
2703 3353 8.065627 TCATATATACTCCCTTCGTCCCATAAT 58.934 37.037 0.00 0.00 0.00 1.28
2704 3354 7.415908 TCATATATACTCCCTTCGTCCCATAA 58.584 38.462 0.00 0.00 0.00 1.90
2705 3355 6.977104 TCATATATACTCCCTTCGTCCCATA 58.023 40.000 0.00 0.00 0.00 2.74
2706 3356 5.838955 TCATATATACTCCCTTCGTCCCAT 58.161 41.667 0.00 0.00 0.00 4.00
2707 3357 5.265290 TCATATATACTCCCTTCGTCCCA 57.735 43.478 0.00 0.00 0.00 4.37
2708 3358 6.039941 CAGATCATATATACTCCCTTCGTCCC 59.960 46.154 0.00 0.00 0.00 4.46
2709 3359 6.829298 TCAGATCATATATACTCCCTTCGTCC 59.171 42.308 0.00 0.00 0.00 4.79
2710 3360 7.867305 TCAGATCATATATACTCCCTTCGTC 57.133 40.000 0.00 0.00 0.00 4.20
2711 3361 8.651589 TTTCAGATCATATATACTCCCTTCGT 57.348 34.615 0.00 0.00 0.00 3.85
2825 3476 3.446570 GCCATGTCAGCTGCCACC 61.447 66.667 9.47 0.00 0.00 4.61
2944 3597 8.948631 TCACATAGAGAAGGATGAAATAACAC 57.051 34.615 0.00 0.00 0.00 3.32
2950 3603 8.156820 TGTCTTTTCACATAGAGAAGGATGAAA 58.843 33.333 0.00 0.00 38.60 2.69
2956 3609 5.121454 GCACTGTCTTTTCACATAGAGAAGG 59.879 44.000 0.00 0.00 38.60 3.46
2960 3613 6.551385 AAAGCACTGTCTTTTCACATAGAG 57.449 37.500 0.00 0.00 32.78 2.43
2974 3627 3.335579 GAGGAACCGATAAAAGCACTGT 58.664 45.455 0.00 0.00 0.00 3.55
2983 3636 4.076394 CCTTTTTGTGGAGGAACCGATAA 58.924 43.478 0.00 0.00 42.61 1.75
3049 3704 7.320443 TGTCTATCCATACTTGAACATTTGC 57.680 36.000 0.00 0.00 0.00 3.68
3129 3785 6.308371 TGGTTTTCTAGAAGTTTAAAGCGG 57.692 37.500 5.12 0.00 0.00 5.52
3130 3786 7.807680 AGATGGTTTTCTAGAAGTTTAAAGCG 58.192 34.615 5.12 0.00 0.00 4.68
3234 3961 2.605823 GGAGAATGTCCAGACGCGATAG 60.606 54.545 15.93 0.46 46.10 2.08
3367 4140 3.084039 GACACCATTCCATCAAGCTGAA 58.916 45.455 0.00 0.00 0.00 3.02
3502 4284 1.758440 GCGGTAGCTGATCCATCCCA 61.758 60.000 0.00 0.00 41.01 4.37
3611 4393 4.424061 TCTTGAAATGACGCAGAAATGG 57.576 40.909 0.00 0.00 0.00 3.16
3679 4462 7.688918 ATCAGTCTTTTTCCCATCTCTAGAT 57.311 36.000 0.00 0.00 34.56 1.98
3696 4480 9.699410 TTATTGAACCAATGGAAATATCAGTCT 57.301 29.630 6.16 0.00 35.54 3.24
3794 4585 2.578786 CATGGCAATAGAGCATCCACA 58.421 47.619 0.00 0.00 33.66 4.17
3795 4586 1.884579 CCATGGCAATAGAGCATCCAC 59.115 52.381 0.00 0.00 33.66 4.02
3796 4587 1.496001 ACCATGGCAATAGAGCATCCA 59.504 47.619 13.04 0.00 33.66 3.41
3941 4733 1.736681 GCAGGACAATTCTGACTCAGC 59.263 52.381 0.62 0.00 34.36 4.26
3984 4780 4.939509 ATTCGTACAAACTGGAAATCGG 57.060 40.909 0.00 0.00 0.00 4.18
3986 4782 7.968405 AGCATTTATTCGTACAAACTGGAAATC 59.032 33.333 0.00 0.00 0.00 2.17
3987 4783 7.826690 AGCATTTATTCGTACAAACTGGAAAT 58.173 30.769 0.00 0.00 0.00 2.17
3988 4784 7.209471 AGCATTTATTCGTACAAACTGGAAA 57.791 32.000 0.00 0.00 0.00 3.13
3989 4785 6.811253 AGCATTTATTCGTACAAACTGGAA 57.189 33.333 0.00 0.00 0.00 3.53
4001 4800 9.591404 TTTGTTGCATTTTAAAGCATTTATTCG 57.409 25.926 3.26 0.00 40.76 3.34
4079 4885 8.298854 GCACCATTGTAAATGATCATATTGCTA 58.701 33.333 9.04 6.90 0.00 3.49
4081 4887 6.924612 TGCACCATTGTAAATGATCATATTGC 59.075 34.615 9.04 9.59 0.00 3.56
4082 4888 8.874744 TTGCACCATTGTAAATGATCATATTG 57.125 30.769 9.04 0.30 0.00 1.90
4173 4979 8.186821 AGCTAAAGCATCAAGTATTTCAATGTC 58.813 33.333 4.54 0.00 45.16 3.06
4197 5007 7.260603 TCCAAAACTAAGTCCTACGTATAAGC 58.739 38.462 0.00 0.00 0.00 3.09
4214 5051 5.016831 ACAGAAGTCCAAAACTCCAAAACT 58.983 37.500 0.00 0.00 37.17 2.66
4215 5052 5.324784 ACAGAAGTCCAAAACTCCAAAAC 57.675 39.130 0.00 0.00 37.17 2.43
4216 5053 7.469537 TTTACAGAAGTCCAAAACTCCAAAA 57.530 32.000 0.00 0.00 37.17 2.44
4218 5055 8.934023 ATATTTACAGAAGTCCAAAACTCCAA 57.066 30.769 0.00 0.00 37.17 3.53
4219 5056 8.934023 AATATTTACAGAAGTCCAAAACTCCA 57.066 30.769 0.00 0.00 37.17 3.86
4220 5057 9.232473 AGAATATTTACAGAAGTCCAAAACTCC 57.768 33.333 0.00 0.00 37.17 3.85
4334 5190 3.999764 ATTTTGGGCCATTATCTCCCT 57.000 42.857 7.26 0.00 40.69 4.20
4337 5193 8.962884 AAAATGTTATTTTGGGCCATTATCTC 57.037 30.769 7.26 0.00 0.00 2.75
4346 5202 6.535150 GCTCTTCCTAAAATGTTATTTTGGGC 59.465 38.462 18.85 7.23 39.13 5.36
4387 5246 7.151999 ACTAGAGTTAGAGTCACATCACAAG 57.848 40.000 0.00 0.00 0.00 3.16
4470 5329 8.131100 TGTGAGAGCTATCTTTTTCAAAAACAG 58.869 33.333 10.18 0.00 35.30 3.16
4472 5332 9.468532 AATGTGAGAGCTATCTTTTTCAAAAAC 57.531 29.630 10.18 0.00 35.30 2.43
4477 5337 8.627208 AAGAAATGTGAGAGCTATCTTTTTCA 57.373 30.769 21.77 11.02 35.30 2.69
4478 5338 9.905171 AAAAGAAATGTGAGAGCTATCTTTTTC 57.095 29.630 10.18 14.25 40.68 2.29
4512 5383 0.764369 AGAACTGTGACAGCTCCCCA 60.764 55.000 13.37 0.00 34.37 4.96
4540 5411 4.837093 ACCTATTTCGGAATGTCCTTCA 57.163 40.909 0.00 0.00 35.41 3.02


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

AutoCloner maintained by Alex Coulton.