Multiple sequence alignment - TraesCS2D01G170400

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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 TraesCS2D01G170400 chr2D 100.000 4215 0 0 960 5174 114532247 114536461 0.000000e+00 7784.0
1 TraesCS2D01G170400 chr2D 100.000 545 0 0 1 545 114531288 114531832 0.000000e+00 1007.0
2 TraesCS2D01G170400 chr2D 92.517 147 10 1 1394 1540 11205571 11205716 5.250000e-50 209.0
3 TraesCS2D01G170400 chr2D 88.608 79 8 1 1984 2061 11205938 11206016 1.530000e-15 95.3
4 TraesCS2D01G170400 chr2A 93.777 4130 160 35 974 5079 115753086 115757142 0.000000e+00 6113.0
5 TraesCS2D01G170400 chr2A 88.008 517 25 13 51 545 115752470 115752971 1.250000e-160 577.0
6 TraesCS2D01G170400 chr2A 90.000 80 5 3 39 117 115752378 115752455 3.300000e-17 100.0
7 TraesCS2D01G170400 chr2B 92.404 4068 204 54 979 5002 164936782 164940788 0.000000e+00 5703.0
8 TraesCS2D01G170400 chr2B 88.914 451 22 9 50 488 164936186 164936620 9.860000e-147 531.0
9 TraesCS2D01G170400 chr2B 96.748 123 4 0 5052 5174 164940788 164940910 6.790000e-49 206.0
10 TraesCS2D01G170400 chr2B 85.294 102 12 3 4914 5015 744182438 744182340 9.170000e-18 102.0
11 TraesCS2D01G170400 chr2B 87.805 82 9 1 1984 2064 535264231 535264312 1.530000e-15 95.3
12 TraesCS2D01G170400 chr2B 100.000 29 0 0 4498 4526 666185491 666185463 3.000000e-03 54.7
13 TraesCS2D01G170400 chr3D 92.763 152 10 1 1389 1540 488862700 488862550 8.720000e-53 219.0
14 TraesCS2D01G170400 chr3D 89.024 82 8 1 1984 2064 488862328 488862247 3.300000e-17 100.0
15 TraesCS2D01G170400 chr6D 92.517 147 10 1 1394 1540 47023785 47023930 5.250000e-50 209.0
16 TraesCS2D01G170400 chr6D 86.585 82 10 1 1984 2064 47024152 47024233 7.140000e-14 89.8
17 TraesCS2D01G170400 chr1D 84.434 212 31 2 1320 1530 305111549 305111759 1.890000e-49 207.0
18 TraesCS2D01G170400 chr5B 90.789 152 13 1 1389 1540 468652140 468652290 8.780000e-48 202.0
19 TraesCS2D01G170400 chr5B 89.744 78 7 1 1988 2064 468652511 468652588 1.190000e-16 99.0
20 TraesCS2D01G170400 chr1A 83.962 212 32 2 1320 1530 382228726 382228936 8.780000e-48 202.0
21 TraesCS2D01G170400 chr1B 83.019 212 34 2 1320 1530 412258137 412257927 1.900000e-44 191.0
22 TraesCS2D01G170400 chr5A 77.157 197 41 4 4817 5011 4788314 4788120 1.520000e-20 111.0
23 TraesCS2D01G170400 chr3A 79.121 91 14 4 4499 4588 42066456 42066370 2.010000e-04 58.4
24 TraesCS2D01G170400 chr3A 79.121 91 14 4 4499 4588 42099845 42099759 2.010000e-04 58.4
25 TraesCS2D01G170400 chr3A 79.121 91 14 4 4499 4588 42129273 42129187 2.010000e-04 58.4
26 TraesCS2D01G170400 chrUn 94.444 36 2 0 4499 4534 116844207 116844172 7.240000e-04 56.5
27 TraesCS2D01G170400 chr4A 100.000 28 0 0 4499 4526 738148050 738148077 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 TraesCS2D01G170400 chr2D 114531288 114536461 5173 False 4395.500000 7784 100.000000 1 5174 2 chr2D.!!$F2 5173
1 TraesCS2D01G170400 chr2A 115752378 115757142 4764 False 2263.333333 6113 90.595000 39 5079 3 chr2A.!!$F1 5040
2 TraesCS2D01G170400 chr2B 164936186 164940910 4724 False 2146.666667 5703 92.688667 50 5174 3 chr2B.!!$F2 5124

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
300 392 0.327924 TATCAACCCACAGCCAGGTG 59.672 55.000 0.00 0.0 36.19 4.00 F
425 527 0.537371 CCAAATCTACCCCGGCATCC 60.537 60.000 0.00 0.0 0.00 3.51 F
451 553 1.147153 CCTTCTCTTCCCCCATCGC 59.853 63.158 0.00 0.0 0.00 4.58 F
1627 1741 0.103937 CCGATCTGCTCCTCTGTTCC 59.896 60.000 0.00 0.0 0.00 3.62 F
1635 1749 0.392193 CTCCTCTGTTCCTTGCGCAT 60.392 55.000 12.75 0.0 0.00 4.73 F
2772 2905 0.384669 GTCGCTGCTTATCCTACCGT 59.615 55.000 0.00 0.0 0.00 4.83 F
2773 2906 1.605710 GTCGCTGCTTATCCTACCGTA 59.394 52.381 0.00 0.0 0.00 4.02 F
3080 3215 1.801913 GCGCACTCGTCAACTCGAT 60.802 57.895 0.30 0.0 39.12 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1736 0.676466 CCTACCATGCGCAAGGAACA 60.676 55.000 36.16 19.36 45.01 3.18 R
1623 1737 0.676782 ACCTACCATGCGCAAGGAAC 60.677 55.000 36.16 0.00 45.01 3.62 R
1634 1748 1.054406 CCATCCGTCCCACCTACCAT 61.054 60.000 0.00 0.00 0.00 3.55 R
2752 2885 0.384309 CGGTAGGATAAGCAGCGACA 59.616 55.000 0.00 0.00 35.31 4.35 R
3065 3200 0.458543 CCCCATCGAGTTGACGAGTG 60.459 60.000 0.00 0.00 45.22 3.51 R
3984 4124 1.026182 GCGATCCACCAATGCACTCA 61.026 55.000 0.00 0.00 0.00 3.41 R
4120 4260 1.134965 GGTGAGTCCTGACTTCATCCG 60.135 57.143 0.63 0.00 42.66 4.18 R
4792 4958 0.471617 ACTCCCTCAGTATGGCATGC 59.528 55.000 9.90 9.90 36.16 4.06 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
20 21 3.893326 GCCTGTAGAAAAATTGCCCAT 57.107 42.857 0.00 0.00 0.00 4.00
21 22 3.524541 GCCTGTAGAAAAATTGCCCATG 58.475 45.455 0.00 0.00 0.00 3.66
22 23 3.195396 GCCTGTAGAAAAATTGCCCATGA 59.805 43.478 0.00 0.00 0.00 3.07
23 24 4.141869 GCCTGTAGAAAAATTGCCCATGAT 60.142 41.667 0.00 0.00 0.00 2.45
24 25 5.627503 GCCTGTAGAAAAATTGCCCATGATT 60.628 40.000 0.00 0.00 0.00 2.57
25 26 6.408869 CCTGTAGAAAAATTGCCCATGATTT 58.591 36.000 0.00 0.00 0.00 2.17
26 27 6.880529 CCTGTAGAAAAATTGCCCATGATTTT 59.119 34.615 0.00 0.00 37.12 1.82
27 28 7.391275 CCTGTAGAAAAATTGCCCATGATTTTT 59.609 33.333 12.76 12.76 44.00 1.94
99 180 8.566260 TGAAAAATTGGCCATGATTAAAACAAG 58.434 29.630 6.09 0.00 0.00 3.16
227 313 1.508632 GTACACACACGCCATCTTGT 58.491 50.000 0.00 0.00 0.00 3.16
247 334 1.147824 CCAGCTGAGCCGATCCATT 59.852 57.895 17.39 0.00 0.00 3.16
248 335 1.164662 CCAGCTGAGCCGATCCATTG 61.165 60.000 17.39 0.00 0.00 2.82
258 345 1.220169 CGATCCATTGCCGAGCTGAG 61.220 60.000 0.00 0.00 0.00 3.35
286 378 3.872511 ATTCCACCGTGTACGTATCAA 57.127 42.857 0.00 0.00 37.74 2.57
300 392 0.327924 TATCAACCCACAGCCAGGTG 59.672 55.000 0.00 0.00 36.19 4.00
375 467 2.163613 CCCCAAAAGTATCTTTCCACGC 59.836 50.000 0.00 0.00 0.00 5.34
376 468 2.163613 CCCAAAAGTATCTTTCCACGCC 59.836 50.000 0.00 0.00 0.00 5.68
419 521 2.550208 GCAGATACCCAAATCTACCCCG 60.550 54.545 0.00 0.00 34.40 5.73
425 527 0.537371 CCAAATCTACCCCGGCATCC 60.537 60.000 0.00 0.00 0.00 3.51
451 553 1.147153 CCTTCTCTTCCCCCATCGC 59.853 63.158 0.00 0.00 0.00 4.58
452 554 1.147153 CTTCTCTTCCCCCATCGCC 59.853 63.158 0.00 0.00 0.00 5.54
453 555 2.650813 CTTCTCTTCCCCCATCGCCG 62.651 65.000 0.00 0.00 0.00 6.46
454 556 4.918201 CTCTTCCCCCATCGCCGC 62.918 72.222 0.00 0.00 0.00 6.53
988 1093 4.825679 CTCCCCTCCCCTCCCCAC 62.826 77.778 0.00 0.00 0.00 4.61
1302 1416 4.838486 GAGGAGCTCGACGCGGTG 62.838 72.222 12.47 1.37 45.59 4.94
1572 1686 4.519540 AACCGAATTGAATTGAACCTGG 57.480 40.909 0.00 0.00 0.00 4.45
1577 1691 4.412207 GAATTGAATTGAACCTGGTACGC 58.588 43.478 0.00 0.00 0.00 4.42
1584 1698 2.918230 GAACCTGGTACGCCCATCGG 62.918 65.000 0.00 0.00 44.15 4.18
1587 1701 3.768185 CTGGTACGCCCATCGGTCG 62.768 68.421 0.00 0.00 44.15 4.79
1622 1736 1.144708 TCTGATCCGATCTGCTCCTCT 59.855 52.381 9.78 0.00 0.00 3.69
1623 1737 1.270274 CTGATCCGATCTGCTCCTCTG 59.730 57.143 9.78 0.00 0.00 3.35
1625 1739 1.686052 GATCCGATCTGCTCCTCTGTT 59.314 52.381 0.75 0.00 0.00 3.16
1626 1740 1.107114 TCCGATCTGCTCCTCTGTTC 58.893 55.000 0.00 0.00 0.00 3.18
1627 1741 0.103937 CCGATCTGCTCCTCTGTTCC 59.896 60.000 0.00 0.00 0.00 3.62
1630 1744 2.738000 CGATCTGCTCCTCTGTTCCTTG 60.738 54.545 0.00 0.00 0.00 3.61
1632 1746 1.004560 TGCTCCTCTGTTCCTTGCG 60.005 57.895 0.00 0.00 0.00 4.85
1634 1748 1.004560 CTCCTCTGTTCCTTGCGCA 60.005 57.895 5.66 5.66 0.00 6.09
1635 1749 0.392193 CTCCTCTGTTCCTTGCGCAT 60.392 55.000 12.75 0.00 0.00 4.73
1730 1847 3.090219 GCCGAGTTACAGGGGCGAT 62.090 63.158 0.00 0.00 35.59 4.58
2114 2234 6.486253 TCTTGTCATGTCAGTAAAGATTGC 57.514 37.500 0.00 0.00 0.00 3.56
2200 2320 9.000486 AGTTGTAGCCTCAAAATTAAGTAGAAC 58.000 33.333 0.00 0.00 0.00 3.01
2226 2346 1.388547 TTGTGTGGTTCTTCACTGCC 58.611 50.000 0.00 0.00 38.40 4.85
2259 2379 7.858382 TGTTTAAACAAATCACATGGTAGTTCG 59.142 33.333 18.54 0.00 35.67 3.95
2510 2630 7.143340 GTCCAATTAAACACCAGTAACCTTTC 58.857 38.462 0.00 0.00 0.00 2.62
2519 2639 5.301805 ACACCAGTAACCTTTCTTGGAATTG 59.698 40.000 0.00 0.00 0.00 2.32
2542 2662 5.695816 TGTTATTTTTACTAAGCCGTGTCGT 59.304 36.000 0.00 0.00 0.00 4.34
2655 2775 5.529800 TGGTGCTCTAACAAAGTTTCTTACC 59.470 40.000 0.00 0.00 0.00 2.85
2668 2788 4.019681 AGTTTCTTACCGGGTCATCATCAA 60.020 41.667 6.32 0.00 0.00 2.57
2694 2814 9.480053 AAATAAGGCATAATAAATGACATGTGC 57.520 29.630 1.15 0.00 0.00 4.57
2696 2816 6.323203 AGGCATAATAAATGACATGTGCTC 57.677 37.500 1.15 0.00 0.00 4.26
2697 2817 5.049198 AGGCATAATAAATGACATGTGCTCG 60.049 40.000 1.15 0.00 0.00 5.03
2699 2819 6.073276 GGCATAATAAATGACATGTGCTCGTA 60.073 38.462 1.15 0.00 0.00 3.43
2700 2820 7.011773 GCATAATAAATGACATGTGCTCGTAG 58.988 38.462 1.15 0.00 0.00 3.51
2701 2821 5.991328 AATAAATGACATGTGCTCGTAGG 57.009 39.130 1.15 0.00 0.00 3.18
2702 2822 3.610040 AAATGACATGTGCTCGTAGGA 57.390 42.857 1.15 0.00 0.00 2.94
2703 2823 3.827008 AATGACATGTGCTCGTAGGAT 57.173 42.857 1.15 0.00 0.00 3.24
2704 2824 3.827008 ATGACATGTGCTCGTAGGATT 57.173 42.857 1.15 0.00 0.00 3.01
2705 2825 3.610040 TGACATGTGCTCGTAGGATTT 57.390 42.857 1.15 0.00 0.00 2.17
2706 2826 3.937814 TGACATGTGCTCGTAGGATTTT 58.062 40.909 1.15 0.00 0.00 1.82
2712 2845 6.823689 ACATGTGCTCGTAGGATTTTTAAGAT 59.176 34.615 0.00 0.00 0.00 2.40
2715 2848 6.535150 TGTGCTCGTAGGATTTTTAAGATCAG 59.465 38.462 0.00 0.00 0.00 2.90
2721 2854 7.768582 TCGTAGGATTTTTAAGATCAGATTGCA 59.231 33.333 0.00 0.00 0.00 4.08
2725 2858 9.857656 AGGATTTTTAAGATCAGATTGCAGATA 57.142 29.630 0.00 0.00 0.00 1.98
2743 2876 4.388165 CAGATAGACCGCAGAAATGCTATG 59.612 45.833 0.00 0.00 0.00 2.23
2746 2879 2.169352 AGACCGCAGAAATGCTATGAGT 59.831 45.455 0.00 0.00 0.00 3.41
2752 2885 5.008019 CCGCAGAAATGCTATGAGTGTATTT 59.992 40.000 0.00 0.00 33.64 1.40
2766 2899 3.871594 AGTGTATTTGTCGCTGCTTATCC 59.128 43.478 0.00 0.00 0.00 2.59
2770 2903 2.596904 TTGTCGCTGCTTATCCTACC 57.403 50.000 0.00 0.00 0.00 3.18
2772 2905 0.384669 GTCGCTGCTTATCCTACCGT 59.615 55.000 0.00 0.00 0.00 4.83
2773 2906 1.605710 GTCGCTGCTTATCCTACCGTA 59.394 52.381 0.00 0.00 0.00 4.02
2849 2984 5.639931 GTCTAAGTTCTTCTGTGGAATGGTC 59.360 44.000 0.00 0.00 0.00 4.02
2903 3038 3.566130 GGCTCTTGGCTTCATGACT 57.434 52.632 0.00 0.00 41.46 3.41
3065 3200 3.660111 GTGTGGGTTGGTGAGCGC 61.660 66.667 0.00 0.00 0.00 5.92
3080 3215 1.801913 GCGCACTCGTCAACTCGAT 60.802 57.895 0.30 0.00 39.12 3.59
3264 3399 2.485814 GACAAGATGAACCCTGCTGAAC 59.514 50.000 0.00 0.00 0.00 3.18
3329 3464 6.601332 GGGAAGGATCACCATAATTACAAGA 58.399 40.000 0.00 0.00 38.94 3.02
3529 3664 6.985188 TCTACTGCATTCCTAAACATTGTC 57.015 37.500 0.00 0.00 0.00 3.18
3537 3672 6.470235 GCATTCCTAAACATTGTCGATGAAAG 59.530 38.462 7.09 1.57 39.15 2.62
3564 3699 3.956199 ACTCATGACATGGCAAAATAGGG 59.044 43.478 4.70 0.00 0.00 3.53
3569 3704 3.088532 GACATGGCAAAATAGGGTGTGA 58.911 45.455 0.00 0.00 0.00 3.58
3721 3856 5.177326 TGACATTTTGCTTGTTGCTCTTTT 58.823 33.333 0.00 0.00 43.37 2.27
3813 3953 8.001881 TGGTTGCAACAAAGAGTTTCTATTTA 57.998 30.769 29.55 0.00 38.74 1.40
3853 3993 7.708752 CCAGTAATTTACAAGTTTCTTTTGGCA 59.291 33.333 9.15 0.00 0.00 4.92
3936 4076 2.946762 GTGCACGACCAAGAAGGC 59.053 61.111 0.00 0.00 43.14 4.35
4260 4400 2.760092 CCATTGAGTTTGTATGGTGGGG 59.240 50.000 0.00 0.00 35.23 4.96
4401 4544 4.828939 TGATCTGTTTGAGCCTTTGTGATT 59.171 37.500 0.00 0.00 0.00 2.57
4659 4806 5.299949 GGAGCACCTTTTGAAATTCACAAT 58.700 37.500 0.00 0.00 0.00 2.71
4661 4808 6.260714 GGAGCACCTTTTGAAATTCACAATTT 59.739 34.615 0.00 0.00 43.43 1.82
4785 4951 8.781067 TGAGAACAATTTTCTGTATCAAAACG 57.219 30.769 7.37 0.00 0.00 3.60
4839 5005 4.553678 AGTTATTTCCGGTAGATCCCTCA 58.446 43.478 0.00 0.00 0.00 3.86
4862 5028 7.683578 TCAATAGGGTATACTAGCTAGACGAA 58.316 38.462 27.45 9.67 0.00 3.85
4910 5076 6.103205 AGGATTACCCATGTTTATGTCCTCAT 59.897 38.462 0.00 0.00 32.34 2.90
4911 5077 7.294720 AGGATTACCCATGTTTATGTCCTCATA 59.705 37.037 0.00 0.00 32.34 2.15
4957 5125 7.381408 TCTTGCTCGTGTATATTGCTTATGTAC 59.619 37.037 0.00 0.00 32.96 2.90
4963 5131 5.411669 GTGTATATTGCTTATGTACAGGGGC 59.588 44.000 0.33 5.79 40.25 5.80
4996 5164 7.016277 GATCGAGGGATTGAGCAATAGCTTTA 61.016 42.308 0.00 0.00 41.86 1.85
5016 5184 9.606631 AGCTTTAAGGTTCTGTATCTAATCAAG 57.393 33.333 0.00 0.00 0.00 3.02
5032 5200 4.927267 ATCAAGTATTCTGACCCCAACA 57.073 40.909 0.00 0.00 0.00 3.33
5040 5208 3.788227 TCTGACCCCAACATATATGGC 57.212 47.619 16.96 0.00 36.58 4.40
5045 5213 3.329520 GACCCCAACATATATGGCTACCA 59.670 47.826 16.96 0.00 36.58 3.25
5098 5266 4.736896 AGCGCCGGTTTCCTCGTC 62.737 66.667 2.29 0.00 0.00 4.20
5144 5312 0.181350 CTCTGGTTAGGTCCATGGGC 59.819 60.000 13.02 10.72 36.84 5.36
5165 5333 1.228429 GCACTACCACCCAAGGCAA 60.228 57.895 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.195396 TCATGGGCAATTTTTCTACAGGC 59.805 43.478 0.00 0.00 0.00 4.85
1 2 5.603170 ATCATGGGCAATTTTTCTACAGG 57.397 39.130 0.00 0.00 0.00 4.00
2 3 7.910441 AAAATCATGGGCAATTTTTCTACAG 57.090 32.000 0.00 0.00 32.57 2.74
28 29 5.521906 TGCAAGGCTTATACACACAAAAA 57.478 34.783 0.00 0.00 0.00 1.94
29 30 5.300539 TCTTGCAAGGCTTATACACACAAAA 59.699 36.000 25.73 0.00 0.00 2.44
30 31 4.824537 TCTTGCAAGGCTTATACACACAAA 59.175 37.500 25.73 0.00 0.00 2.83
31 32 4.393834 TCTTGCAAGGCTTATACACACAA 58.606 39.130 25.73 0.00 0.00 3.33
32 33 4.014569 TCTTGCAAGGCTTATACACACA 57.985 40.909 25.73 0.00 0.00 3.72
33 34 5.371115 TTTCTTGCAAGGCTTATACACAC 57.629 39.130 25.73 0.00 0.00 3.82
34 35 6.398234 TTTTTCTTGCAAGGCTTATACACA 57.602 33.333 25.73 0.00 0.00 3.72
35 36 7.090173 TCATTTTTCTTGCAAGGCTTATACAC 58.910 34.615 25.73 0.00 0.00 2.90
36 37 7.225784 TCATTTTTCTTGCAAGGCTTATACA 57.774 32.000 25.73 1.09 0.00 2.29
37 38 6.254373 GCTCATTTTTCTTGCAAGGCTTATAC 59.746 38.462 25.73 5.46 0.00 1.47
43 44 2.758009 TGCTCATTTTTCTTGCAAGGC 58.242 42.857 25.73 17.91 0.00 4.35
227 313 3.157252 GGATCGGCTCAGCTGGGA 61.157 66.667 20.53 8.94 35.34 4.37
266 358 3.514645 GTTGATACGTACACGGTGGAAT 58.485 45.455 13.48 0.00 44.95 3.01
320 412 0.609151 TATGACAAAAGGGTCCGCGA 59.391 50.000 8.23 0.00 36.97 5.87
358 450 3.482436 TGTGGCGTGGAAAGATACTTTT 58.518 40.909 0.00 0.00 0.00 2.27
365 457 1.472552 CGGATATGTGGCGTGGAAAGA 60.473 52.381 0.00 0.00 0.00 2.52
400 502 2.335933 CCGGGGTAGATTTGGGTATCT 58.664 52.381 0.00 0.00 38.41 1.98
401 503 1.271217 GCCGGGGTAGATTTGGGTATC 60.271 57.143 2.18 0.00 0.00 2.24
402 504 0.769247 GCCGGGGTAGATTTGGGTAT 59.231 55.000 2.18 0.00 0.00 2.73
403 505 0.620990 TGCCGGGGTAGATTTGGGTA 60.621 55.000 2.18 0.00 0.00 3.69
404 506 1.286305 ATGCCGGGGTAGATTTGGGT 61.286 55.000 2.18 0.00 0.00 4.51
405 507 0.537371 GATGCCGGGGTAGATTTGGG 60.537 60.000 2.18 0.00 0.00 4.12
406 508 0.537371 GGATGCCGGGGTAGATTTGG 60.537 60.000 2.18 0.00 0.00 3.28
433 535 1.147153 GCGATGGGGGAAGAGAAGG 59.853 63.158 0.00 0.00 0.00 3.46
434 536 1.147153 GGCGATGGGGGAAGAGAAG 59.853 63.158 0.00 0.00 0.00 2.85
1302 1416 0.736053 AGGTCTCGATCGTCTTGAGC 59.264 55.000 15.94 16.80 35.58 4.26
1577 1691 1.810151 ACAAATCAAACGACCGATGGG 59.190 47.619 0.00 0.00 40.11 4.00
1584 1698 5.845985 TCAGATCTCACAAATCAAACGAC 57.154 39.130 0.00 0.00 0.00 4.34
1587 1701 5.582269 TCGGATCAGATCTCACAAATCAAAC 59.418 40.000 10.36 0.00 0.00 2.93
1618 1732 1.651240 CCATGCGCAAGGAACAGAGG 61.651 60.000 27.05 7.26 45.01 3.69
1622 1736 0.676466 CCTACCATGCGCAAGGAACA 60.676 55.000 36.16 19.36 45.01 3.18
1623 1737 0.676782 ACCTACCATGCGCAAGGAAC 60.677 55.000 36.16 0.00 45.01 3.62
1625 1739 1.078497 CACCTACCATGCGCAAGGA 60.078 57.895 36.16 19.00 46.91 3.36
1626 1740 2.114670 CCACCTACCATGCGCAAGG 61.115 63.158 28.96 28.96 38.28 3.61
1627 1741 2.114670 CCCACCTACCATGCGCAAG 61.115 63.158 17.11 10.85 43.44 4.01
1630 1744 2.513897 GTCCCACCTACCATGCGC 60.514 66.667 0.00 0.00 0.00 6.09
1632 1746 1.696097 ATCCGTCCCACCTACCATGC 61.696 60.000 0.00 0.00 0.00 4.06
1634 1748 1.054406 CCATCCGTCCCACCTACCAT 61.054 60.000 0.00 0.00 0.00 3.55
1635 1749 1.687840 CCATCCGTCCCACCTACCA 60.688 63.158 0.00 0.00 0.00 3.25
1868 1985 3.143675 CAGGTTCCACTGGATGACG 57.856 57.895 0.00 0.00 34.84 4.35
2114 2234 7.651304 GTGTCATACTCTCAAGAATATGTCCAG 59.349 40.741 7.99 0.00 36.13 3.86
2200 2320 3.859386 GTGAAGAACCACACAAAAAGCTG 59.141 43.478 0.00 0.00 37.04 4.24
2226 2346 6.841443 TGTGATTTGTTTAAACATTGGCAG 57.159 33.333 21.17 0.00 38.95 4.85
2259 2379 3.947834 CCAACTACTGATTGATGAACCCC 59.052 47.826 0.00 0.00 0.00 4.95
2510 2630 9.072294 CGGCTTAGTAAAAATAACAATTCCAAG 57.928 33.333 0.00 0.00 0.00 3.61
2519 2639 6.011277 CACGACACGGCTTAGTAAAAATAAC 58.989 40.000 0.00 0.00 0.00 1.89
2655 2775 3.631686 TGCCTTATTTTGATGATGACCCG 59.368 43.478 0.00 0.00 0.00 5.28
2668 2788 9.480053 GCACATGTCATTTATTATGCCTTATTT 57.520 29.630 0.00 0.00 0.00 1.40
2685 2805 3.610040 AAATCCTACGAGCACATGTCA 57.390 42.857 0.00 0.00 0.00 3.58
2686 2806 4.946784 AAAAATCCTACGAGCACATGTC 57.053 40.909 0.00 0.00 0.00 3.06
2687 2807 6.170506 TCTTAAAAATCCTACGAGCACATGT 58.829 36.000 0.00 0.00 0.00 3.21
2688 2808 6.662414 TCTTAAAAATCCTACGAGCACATG 57.338 37.500 0.00 0.00 0.00 3.21
2689 2809 7.047891 TGATCTTAAAAATCCTACGAGCACAT 58.952 34.615 0.00 0.00 0.00 3.21
2690 2810 6.403049 TGATCTTAAAAATCCTACGAGCACA 58.597 36.000 0.00 0.00 0.00 4.57
2691 2811 6.757010 TCTGATCTTAAAAATCCTACGAGCAC 59.243 38.462 0.00 0.00 0.00 4.40
2694 2814 8.279103 GCAATCTGATCTTAAAAATCCTACGAG 58.721 37.037 0.00 0.00 0.00 4.18
2696 2816 7.919690 TGCAATCTGATCTTAAAAATCCTACG 58.080 34.615 0.00 0.00 0.00 3.51
2697 2817 9.113838 TCTGCAATCTGATCTTAAAAATCCTAC 57.886 33.333 0.00 0.00 0.00 3.18
2699 2819 8.763984 ATCTGCAATCTGATCTTAAAAATCCT 57.236 30.769 0.00 0.00 0.00 3.24
2703 2823 9.113838 GGTCTATCTGCAATCTGATCTTAAAAA 57.886 33.333 0.00 0.00 33.66 1.94
2704 2824 7.439356 CGGTCTATCTGCAATCTGATCTTAAAA 59.561 37.037 0.00 0.00 33.66 1.52
2705 2825 6.925718 CGGTCTATCTGCAATCTGATCTTAAA 59.074 38.462 0.00 0.00 33.66 1.52
2706 2826 6.450545 CGGTCTATCTGCAATCTGATCTTAA 58.549 40.000 0.00 0.00 33.66 1.85
2712 2845 2.515926 GCGGTCTATCTGCAATCTGA 57.484 50.000 0.00 0.00 46.78 3.27
2743 2876 4.025647 GGATAAGCAGCGACAAATACACTC 60.026 45.833 0.00 0.00 0.00 3.51
2746 2879 4.137116 AGGATAAGCAGCGACAAATACA 57.863 40.909 0.00 0.00 0.00 2.29
2752 2885 0.384309 CGGTAGGATAAGCAGCGACA 59.616 55.000 0.00 0.00 35.31 4.35
2833 2968 5.529289 ACCTATAGACCATTCCACAGAAGA 58.471 41.667 0.00 0.00 34.86 2.87
2849 2984 2.691526 TGCCAACTCACGGTACCTATAG 59.308 50.000 10.90 6.53 0.00 1.31
2882 3017 0.986527 TCATGAAGCCAAGAGCCTCA 59.013 50.000 0.00 0.00 45.86 3.86
2918 3053 3.323691 TCGTCATTATCGGATGGTCCATT 59.676 43.478 5.65 0.00 35.91 3.16
3065 3200 0.458543 CCCCATCGAGTTGACGAGTG 60.459 60.000 0.00 0.00 45.22 3.51
3080 3215 1.358787 AGGAATTCAACATGAGCCCCA 59.641 47.619 7.93 0.00 0.00 4.96
3186 3321 9.829507 TTTAAATTTCATCATCCAAAACACACT 57.170 25.926 0.00 0.00 0.00 3.55
3233 3368 4.262894 GGGTTCATCTTGTCACTCACCTAA 60.263 45.833 0.00 0.00 0.00 2.69
3264 3399 4.778534 AAATGTCAATCAGCTTCACCAG 57.221 40.909 0.00 0.00 0.00 4.00
3329 3464 1.002069 TCATGTTCTCAGCCCCCATT 58.998 50.000 0.00 0.00 0.00 3.16
3529 3664 5.596268 TGTCATGAGTTTCACTTTCATCG 57.404 39.130 0.00 0.00 29.48 3.84
3537 3672 3.921119 TTGCCATGTCATGAGTTTCAC 57.079 42.857 14.67 0.00 0.00 3.18
3569 3704 8.735692 AAACATTTGATTGTGAAAGAAATGGT 57.264 26.923 0.00 0.00 38.01 3.55
3634 3769 6.211184 TCCATAGGCAGTTCAATCAACAATTT 59.789 34.615 0.00 0.00 37.48 1.82
3635 3770 5.716228 TCCATAGGCAGTTCAATCAACAATT 59.284 36.000 0.00 0.00 37.48 2.32
3636 3771 5.263599 TCCATAGGCAGTTCAATCAACAAT 58.736 37.500 0.00 0.00 37.48 2.71
3637 3772 4.661222 TCCATAGGCAGTTCAATCAACAA 58.339 39.130 0.00 0.00 37.48 2.83
3721 3856 5.991933 TTTTGTAGGGATTTATGCAGCAA 57.008 34.783 0.00 0.00 0.00 3.91
3860 4000 7.190920 ACACAAAGTTAATGTTAGAGCAGTC 57.809 36.000 0.00 0.00 0.00 3.51
3981 4121 1.741706 GATCCACCAATGCACTCAGTG 59.258 52.381 0.00 0.00 37.97 3.66
3984 4124 1.026182 GCGATCCACCAATGCACTCA 61.026 55.000 0.00 0.00 0.00 3.41
3993 4133 2.994995 ACAGTCCGCGATCCACCA 60.995 61.111 8.23 0.00 0.00 4.17
4120 4260 1.134965 GGTGAGTCCTGACTTCATCCG 60.135 57.143 0.63 0.00 42.66 4.18
4326 4466 3.243941 ACATAGTGCAACACCACGAGTAA 60.244 43.478 0.00 0.00 41.43 2.24
4447 4590 8.812513 TCACCAAATAGATGAAACAATGAGAT 57.187 30.769 0.00 0.00 0.00 2.75
4458 4601 9.330063 GACAGATTTACATCACCAAATAGATGA 57.670 33.333 9.17 0.00 43.28 2.92
4598 4744 7.627585 ATGTTCACAATTCAGAAAATGTTCG 57.372 32.000 2.90 0.00 38.90 3.95
4631 4778 4.769345 ATTTCAAAAGGTGCTCCCAAAA 57.231 36.364 0.00 0.00 34.66 2.44
4768 4934 7.013529 GCGTCTTACGTTTTGATACAGAAAAT 58.986 34.615 0.00 0.00 44.73 1.82
4785 4951 2.797156 CTCAGTATGGCATGCGTCTTAC 59.203 50.000 12.44 11.05 36.16 2.34
4792 4958 0.471617 ACTCCCTCAGTATGGCATGC 59.528 55.000 9.90 9.90 36.16 4.06
4850 5016 8.687242 TCCCATTTGATATATTCGTCTAGCTAG 58.313 37.037 15.01 15.01 0.00 3.42
4852 5018 7.482169 TCCCATTTGATATATTCGTCTAGCT 57.518 36.000 0.00 0.00 0.00 3.32
4910 5076 7.582828 GCAAGAAATAGGGTTTTACCTCCTCTA 60.583 40.741 0.00 0.00 42.09 2.43
4911 5077 6.722328 CAAGAAATAGGGTTTTACCTCCTCT 58.278 40.000 0.00 0.00 42.09 3.69
4957 5125 2.555199 CTCGATCTTTGTAAGCCCCTG 58.445 52.381 0.00 0.00 0.00 4.45
4963 5131 4.509600 GCTCAATCCCTCGATCTTTGTAAG 59.490 45.833 0.00 0.00 0.00 2.34
5014 5182 7.461749 CCATATATGTTGGGGTCAGAATACTT 58.538 38.462 11.73 0.00 0.00 2.24
5016 5184 5.648092 GCCATATATGTTGGGGTCAGAATAC 59.352 44.000 11.73 0.00 34.66 1.89
5023 5191 3.329520 TGGTAGCCATATATGTTGGGGTC 59.670 47.826 11.73 0.00 34.66 4.46
5032 5200 5.198840 ACCCTAGATCCTGGTAGCCATATAT 59.801 44.000 0.00 0.00 30.82 0.86
5040 5208 8.437274 AATTATGTAACCCTAGATCCTGGTAG 57.563 38.462 0.00 0.00 0.00 3.18
5045 5213 9.536510 GACTAGAATTATGTAACCCTAGATCCT 57.463 37.037 0.00 0.00 31.05 3.24
5086 5254 2.654912 GCACACGACGAGGAAACCG 61.655 63.158 0.00 0.00 0.00 4.44
5098 5266 1.002134 AGAGGATTTGGGGCACACG 60.002 57.895 0.00 0.00 0.00 4.49
5144 5312 2.046314 CTTGGGTGGTAGTGCCGG 60.046 66.667 0.00 0.00 41.21 6.13


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

AutoCloner maintained by Alex Coulton.