Multiple sequence alignment - TraesCS7A01G428400

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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 TraesCS7A01G428400 chr7A 100.000 3177 0 0 1 3177 621858860 621855684 0.000000e+00 5867
1 TraesCS7A01G428400 chr7A 86.447 546 39 19 108 621 116010775 116010233 1.650000e-157 566
2 TraesCS7A01G428400 chr7A 91.667 300 19 2 321 615 194463248 194463546 8.200000e-111 411
3 TraesCS7A01G428400 chr7B 92.304 2326 108 32 776 3088 583623543 583621276 0.000000e+00 3238
4 TraesCS7A01G428400 chr7B 89.796 294 21 3 1987 2271 583559445 583559152 5.010000e-98 368
5 TraesCS7A01G428400 chr7B 85.882 170 4 2 621 770 583623788 583623619 2.540000e-36 163
6 TraesCS7A01G428400 chr7B 91.964 112 8 1 2558 2669 583558014 583557904 4.240000e-34 156
7 TraesCS7A01G428400 chr7D 91.599 2345 129 34 818 3133 540507932 540505627 0.000000e+00 3177
8 TraesCS7A01G428400 chr7D 82.857 175 6 8 624 774 540508202 540508028 5.530000e-28 135
9 TraesCS7A01G428400 chr3A 91.590 547 36 6 85 621 300602411 300602957 0.000000e+00 747
10 TraesCS7A01G428400 chr3A 91.045 536 41 3 92 621 251370077 251369543 0.000000e+00 717
11 TraesCS7A01G428400 chr3A 90.057 523 46 2 105 621 240935136 240934614 0.000000e+00 673
12 TraesCS7A01G428400 chr3A 87.857 560 34 9 93 621 21422559 21423115 7.480000e-176 627
13 TraesCS7A01G428400 chr3A 87.701 561 36 17 93 622 269502252 269501694 9.680000e-175 623
14 TraesCS7A01G428400 chrUn 90.370 540 42 6 89 618 113056051 113056590 0.000000e+00 701
15 TraesCS7A01G428400 chr5A 88.023 526 33 7 93 589 380159779 380159255 2.110000e-166 595
16 TraesCS7A01G428400 chr2D 86.511 556 44 13 90 615 645180997 645181551 1.640000e-162 582
17 TraesCS7A01G428400 chr3D 86.213 544 41 15 110 621 604877716 604878257 2.770000e-155 558
18 TraesCS7A01G428400 chr5D 83.865 564 58 12 89 621 321607015 321606454 1.020000e-139 507
19 TraesCS7A01G428400 chr6A 92.213 244 17 2 89 331 39457500 39457258 8.440000e-91 344
20 TraesCS7A01G428400 chr6A 83.646 373 52 4 1801 2167 15582478 15582109 3.030000e-90 342
21 TraesCS7A01G428400 chr6A 81.016 374 62 5 1801 2168 15577100 15576730 4.010000e-74 289
22 TraesCS7A01G428400 chr6A 83.663 202 24 4 1329 1529 15577903 15577710 7.000000e-42 182
23 TraesCS7A01G428400 chr6B 83.582 201 26 2 1329 1529 26082140 26082333 7.000000e-42 182
24 TraesCS7A01G428400 chr6D 82.587 201 28 2 1329 1529 14289456 14289263 1.520000e-38 171


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 TraesCS7A01G428400 chr7A 621855684 621858860 3176 True 5867.0 5867 100.0000 1 3177 1 chr7A.!!$R2 3176
1 TraesCS7A01G428400 chr7A 116010233 116010775 542 True 566.0 566 86.4470 108 621 1 chr7A.!!$R1 513
2 TraesCS7A01G428400 chr7B 583621276 583623788 2512 True 1700.5 3238 89.0930 621 3088 2 chr7B.!!$R2 2467
3 TraesCS7A01G428400 chr7B 583557904 583559445 1541 True 262.0 368 90.8800 1987 2669 2 chr7B.!!$R1 682
4 TraesCS7A01G428400 chr7D 540505627 540508202 2575 True 1656.0 3177 87.2280 624 3133 2 chr7D.!!$R1 2509
5 TraesCS7A01G428400 chr3A 300602411 300602957 546 False 747.0 747 91.5900 85 621 1 chr3A.!!$F2 536
6 TraesCS7A01G428400 chr3A 251369543 251370077 534 True 717.0 717 91.0450 92 621 1 chr3A.!!$R2 529
7 TraesCS7A01G428400 chr3A 240934614 240935136 522 True 673.0 673 90.0570 105 621 1 chr3A.!!$R1 516
8 TraesCS7A01G428400 chr3A 21422559 21423115 556 False 627.0 627 87.8570 93 621 1 chr3A.!!$F1 528
9 TraesCS7A01G428400 chr3A 269501694 269502252 558 True 623.0 623 87.7010 93 622 1 chr3A.!!$R3 529
10 TraesCS7A01G428400 chrUn 113056051 113056590 539 False 701.0 701 90.3700 89 618 1 chrUn.!!$F1 529
11 TraesCS7A01G428400 chr5A 380159255 380159779 524 True 595.0 595 88.0230 93 589 1 chr5A.!!$R1 496
12 TraesCS7A01G428400 chr2D 645180997 645181551 554 False 582.0 582 86.5110 90 615 1 chr2D.!!$F1 525
13 TraesCS7A01G428400 chr3D 604877716 604878257 541 False 558.0 558 86.2130 110 621 1 chr3D.!!$F1 511
14 TraesCS7A01G428400 chr5D 321606454 321607015 561 True 507.0 507 83.8650 89 621 1 chr5D.!!$R1 532
15 TraesCS7A01G428400 chr6A 15576730 15577903 1173 True 235.5 289 82.3395 1329 2168 2 chr6A.!!$R3 839

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
79 80 0.324645 AAATCATGGACCACCCTGGC 60.325 55.0 0.0 0.0 42.67 4.85 F
901 1094 0.445043 GCTAAAACCGGTAAGGCACG 59.555 55.0 8.0 0.0 46.52 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 2218 0.039764 TCATGTCGGTCTGGGAGAGT 59.960 55.0 0.00 0.0 0.00 3.24 R
2788 4288 0.033781 TTGCAAATTGCTGGAGCCAC 59.966 50.0 19.34 0.0 45.31 5.01 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
26 27 9.979578 TTTGTGTTTAATTGCTCATGTTAGATT 57.020 25.926 0.00 0.00 0.00 2.40
27 28 9.979578 TTGTGTTTAATTGCTCATGTTAGATTT 57.020 25.926 0.00 0.00 0.00 2.17
28 29 9.979578 TGTGTTTAATTGCTCATGTTAGATTTT 57.020 25.926 0.00 0.00 0.00 1.82
71 72 9.686683 AATATGGCTATAGTAAAATCATGGACC 57.313 33.333 0.84 0.00 0.00 4.46
72 73 6.508030 TGGCTATAGTAAAATCATGGACCA 57.492 37.500 0.00 0.00 0.00 4.02
73 74 6.296026 TGGCTATAGTAAAATCATGGACCAC 58.704 40.000 0.00 0.00 0.00 4.16
74 75 5.705905 GGCTATAGTAAAATCATGGACCACC 59.294 44.000 0.00 0.00 0.00 4.61
75 76 5.705905 GCTATAGTAAAATCATGGACCACCC 59.294 44.000 0.00 0.00 34.81 4.61
76 77 5.994416 ATAGTAAAATCATGGACCACCCT 57.006 39.130 0.00 0.00 35.38 4.34
77 78 3.968265 AGTAAAATCATGGACCACCCTG 58.032 45.455 0.00 0.00 35.38 4.45
78 79 2.236489 AAAATCATGGACCACCCTGG 57.764 50.000 0.00 0.00 45.02 4.45
79 80 0.324645 AAATCATGGACCACCCTGGC 60.325 55.000 0.00 0.00 42.67 4.85
80 81 2.228841 AATCATGGACCACCCTGGCC 62.229 60.000 0.00 0.00 42.67 5.36
81 82 4.447342 CATGGACCACCCTGGCCC 62.447 72.222 0.00 0.00 42.67 5.80
86 87 3.622263 ACCACCCTGGCCCCTCTA 61.622 66.667 0.00 0.00 42.67 2.43
87 88 2.770048 CCACCCTGGCCCCTCTAG 60.770 72.222 0.00 0.00 0.00 2.43
182 186 2.224549 TGTTTCTGACATTAAACCCGCG 59.775 45.455 0.00 0.00 35.23 6.46
379 438 3.278574 TGATTCGGATTGTGGATGAACC 58.721 45.455 0.00 0.00 39.54 3.62
529 593 1.889829 CCATCTTTGTTTGGGCCGTAA 59.110 47.619 0.00 0.00 0.00 3.18
533 597 3.818180 TCTTTGTTTGGGCCGTAACTAA 58.182 40.909 18.46 16.16 0.00 2.24
602 667 1.886886 TCTTTACTCCCGTTGCAACC 58.113 50.000 23.42 6.48 0.00 3.77
618 683 1.420532 AACCCACGGACCCTTTGCTA 61.421 55.000 0.00 0.00 0.00 3.49
619 684 1.078426 CCCACGGACCCTTTGCTAG 60.078 63.158 0.00 0.00 0.00 3.42
712 801 0.725117 CAATTCCTCGGCCGTTACAC 59.275 55.000 27.15 0.00 0.00 2.90
774 915 4.213694 CACGAGCATTATCTCCTACGTACT 59.786 45.833 0.00 0.00 0.00 2.73
875 1068 4.021456 CCACGTGCAACCTCCATATATCTA 60.021 45.833 10.91 0.00 0.00 1.98
898 1091 1.004595 CGAGCTAAAACCGGTAAGGC 58.995 55.000 8.00 10.64 46.52 4.35
899 1092 1.673626 CGAGCTAAAACCGGTAAGGCA 60.674 52.381 8.00 0.00 46.52 4.75
900 1093 1.736126 GAGCTAAAACCGGTAAGGCAC 59.264 52.381 8.00 5.49 46.52 5.01
901 1094 0.445043 GCTAAAACCGGTAAGGCACG 59.555 55.000 8.00 0.00 46.52 5.34
902 1095 1.940752 GCTAAAACCGGTAAGGCACGA 60.941 52.381 8.00 0.00 46.52 4.35
903 1096 1.728425 CTAAAACCGGTAAGGCACGAC 59.272 52.381 8.00 0.00 46.52 4.34
904 1097 0.886043 AAAACCGGTAAGGCACGACC 60.886 55.000 8.00 0.00 46.52 4.79
908 1101 3.116531 GGTAAGGCACGACCGCAC 61.117 66.667 0.00 0.00 46.52 5.34
909 1102 3.475774 GTAAGGCACGACCGCACG 61.476 66.667 0.00 0.00 46.52 5.34
910 1103 3.672447 TAAGGCACGACCGCACGA 61.672 61.111 6.49 0.00 46.52 4.35
911 1104 3.620300 TAAGGCACGACCGCACGAG 62.620 63.158 6.49 0.31 46.52 4.18
944 1142 2.736531 GCCAGCCACACTTTTGGG 59.263 61.111 0.00 0.00 37.10 4.12
1176 1380 1.452108 GGCCCAGTCCCAAATCTCG 60.452 63.158 0.00 0.00 0.00 4.04
1181 1385 3.202706 GTCCCAAATCTCGGCGGC 61.203 66.667 7.21 0.00 0.00 6.53
1243 1447 2.847327 ACACAACCTCTGATCACTGG 57.153 50.000 7.49 7.49 0.00 4.00
1258 1462 4.838152 TGGCCGATTGAGCTCGCC 62.838 66.667 19.32 19.32 37.33 5.54
1267 1471 0.532573 TTGAGCTCGCCCTTGTAGAG 59.467 55.000 9.64 0.00 35.28 2.43
1268 1472 0.612174 TGAGCTCGCCCTTGTAGAGT 60.612 55.000 9.64 0.00 34.69 3.24
1310 1514 8.781196 TGAGTTGATGACGTAGGTATCTATAAC 58.219 37.037 0.00 0.00 0.00 1.89
1314 1518 8.687292 TGATGACGTAGGTATCTATAACTTGT 57.313 34.615 0.00 0.00 31.60 3.16
1320 1524 6.976349 CGTAGGTATCTATAACTTGTTGTGCA 59.024 38.462 0.00 0.00 31.60 4.57
1321 1525 7.043590 CGTAGGTATCTATAACTTGTTGTGCAC 60.044 40.741 10.75 10.75 31.60 4.57
1322 1526 5.810587 AGGTATCTATAACTTGTTGTGCACG 59.189 40.000 13.13 0.00 0.00 5.34
1323 1527 5.579511 GGTATCTATAACTTGTTGTGCACGT 59.420 40.000 13.13 0.00 0.00 4.49
1659 2218 0.911525 CCTTCTTCTCAGGCCTGGGA 60.912 60.000 32.25 32.25 38.52 4.37
1713 2272 6.727824 GGTAACTGAAGTAGTACGTACTCA 57.272 41.667 30.53 20.62 41.50 3.41
1728 2287 4.523173 ACGTACTCATCAACTTCTCCTGAA 59.477 41.667 0.00 0.00 0.00 3.02
1876 2446 2.348104 CGACCCGACCATGGACTCA 61.348 63.158 21.47 0.00 0.00 3.41
2029 2602 2.738480 GTGCTGTACACGGACCCA 59.262 61.111 0.00 0.00 40.07 4.51
2071 2644 2.918802 TACGCGTCCAACCAGGGT 60.919 61.111 18.63 0.00 38.24 4.34
2187 2763 6.032717 GGTACACGAATTAGTTACAGAGTCC 58.967 44.000 0.00 0.00 0.00 3.85
2192 2768 2.226962 TTAGTTACAGAGTCCCCGCT 57.773 50.000 0.00 0.00 0.00 5.52
2219 2797 1.971481 TGCTGATGCTCACACAGTTT 58.029 45.000 0.00 0.00 40.48 2.66
2220 2798 2.300433 TGCTGATGCTCACACAGTTTT 58.700 42.857 0.00 0.00 40.48 2.43
2245 2829 1.229428 AACTGTCCATGACGCAACTG 58.771 50.000 0.00 0.00 34.95 3.16
2319 2903 4.276926 GCCCATGATGTCTTCAACTAATCC 59.723 45.833 0.00 0.00 38.03 3.01
2337 2921 3.981071 TCCACTGTAAGATGTCCTTGG 57.019 47.619 0.00 0.00 37.43 3.61
2439 3023 2.545946 GAGTCAGACTCCAGCACAAAAC 59.454 50.000 18.76 0.00 39.28 2.43
2669 4169 0.242017 GTGAGCATGTTCAGGTTGCC 59.758 55.000 13.02 0.00 37.07 4.52
2670 4170 0.895100 TGAGCATGTTCAGGTTGCCC 60.895 55.000 8.32 0.00 37.07 5.36
2671 4171 0.895100 GAGCATGTTCAGGTTGCCCA 60.895 55.000 4.47 0.00 37.07 5.36
2737 4237 8.466617 TCTTCCTTTGTACTACTCCTATGATC 57.533 38.462 0.00 0.00 0.00 2.92
2755 4255 2.791383 TCCTTGCGGATGTTTTTGTG 57.209 45.000 0.00 0.00 33.30 3.33
2756 4256 2.028130 TCCTTGCGGATGTTTTTGTGT 58.972 42.857 0.00 0.00 33.30 3.72
2757 4257 3.215151 TCCTTGCGGATGTTTTTGTGTA 58.785 40.909 0.00 0.00 33.30 2.90
2766 4266 6.523201 GCGGATGTTTTTGTGTAGTATTTCAG 59.477 38.462 0.00 0.00 0.00 3.02
2792 4292 3.793559 AGTGGATTTCAGTATACGTGGC 58.206 45.455 0.00 0.00 0.00 5.01
2793 4293 3.451178 AGTGGATTTCAGTATACGTGGCT 59.549 43.478 0.00 0.00 0.00 4.75
2796 4296 3.181469 GGATTTCAGTATACGTGGCTCCA 60.181 47.826 0.00 0.00 0.00 3.86
2797 4297 3.520290 TTTCAGTATACGTGGCTCCAG 57.480 47.619 0.00 0.00 0.00 3.86
2823 4323 7.534282 CAATTTGCAAAAACCTACCAAAACTT 58.466 30.769 17.19 0.00 0.00 2.66
2824 4324 6.487689 TTTGCAAAAACCTACCAAAACTTG 57.512 33.333 10.02 0.00 0.00 3.16
2826 4326 4.932200 TGCAAAAACCTACCAAAACTTGTG 59.068 37.500 0.00 0.00 0.00 3.33
2866 4366 1.544759 GGTCACTTAACCACCCACCAG 60.545 57.143 0.00 0.00 39.27 4.00
2889 4389 5.942826 AGAAAGATCTTGCCTGTTTTCCTAG 59.057 40.000 9.17 0.00 29.15 3.02
2995 4502 5.161886 TGGATGGATTGATACATAGTGGGA 58.838 41.667 0.00 0.00 29.60 4.37
3009 4516 0.524862 GTGGGAAGCATGACAAGCTG 59.475 55.000 5.85 0.00 42.53 4.24
3048 4555 0.904649 TGTGGTAGTGCTGATGGAGG 59.095 55.000 0.00 0.00 0.00 4.30
3088 4595 0.973632 TGCGGTGCTAGAGGAAAAGA 59.026 50.000 0.00 0.00 0.00 2.52
3090 4597 2.224426 TGCGGTGCTAGAGGAAAAGAAA 60.224 45.455 0.00 0.00 0.00 2.52
3092 4599 3.440522 GCGGTGCTAGAGGAAAAGAAAAT 59.559 43.478 0.00 0.00 0.00 1.82
3093 4600 4.634443 GCGGTGCTAGAGGAAAAGAAAATA 59.366 41.667 0.00 0.00 0.00 1.40
3094 4601 5.220681 GCGGTGCTAGAGGAAAAGAAAATAG 60.221 44.000 0.00 0.00 0.00 1.73
3095 4602 6.106673 CGGTGCTAGAGGAAAAGAAAATAGA 58.893 40.000 0.00 0.00 0.00 1.98
3097 4604 7.281100 CGGTGCTAGAGGAAAAGAAAATAGAAT 59.719 37.037 0.00 0.00 0.00 2.40
3099 4606 8.951243 GTGCTAGAGGAAAAGAAAATAGAATGT 58.049 33.333 0.00 0.00 0.00 2.71
3100 4607 9.520515 TGCTAGAGGAAAAGAAAATAGAATGTT 57.479 29.630 0.00 0.00 0.00 2.71
3101 4608 9.995957 GCTAGAGGAAAAGAAAATAGAATGTTC 57.004 33.333 0.00 0.00 0.00 3.18
3120 4631 7.931015 ATGTTCCATAGGGTGTAGATCTAAA 57.069 36.000 3.40 0.00 34.93 1.85
3126 4637 8.651389 TCCATAGGGTGTAGATCTAAAGATTTG 58.349 37.037 3.40 0.00 33.06 2.32
3139 4650 9.937175 GATCTAAAGATTTGGAAAATAACTCCG 57.063 33.333 0.00 0.00 33.48 4.63
3140 4651 7.758495 TCTAAAGATTTGGAAAATAACTCCGC 58.242 34.615 0.00 0.00 35.55 5.54
3141 4652 5.975693 AAGATTTGGAAAATAACTCCGCA 57.024 34.783 0.00 0.00 35.55 5.69
3142 4653 5.975693 AGATTTGGAAAATAACTCCGCAA 57.024 34.783 0.00 0.00 35.55 4.85
3143 4654 6.339587 AGATTTGGAAAATAACTCCGCAAA 57.660 33.333 0.00 0.00 35.55 3.68
3144 4655 6.754193 AGATTTGGAAAATAACTCCGCAAAA 58.246 32.000 0.00 0.00 35.55 2.44
3145 4656 7.213678 AGATTTGGAAAATAACTCCGCAAAAA 58.786 30.769 0.00 0.00 35.55 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.979578 AATCTAACATGAGCAATTAAACACAAA 57.020 25.926 0.00 0.00 0.00 2.83
2 3 9.979578 AAAATCTAACATGAGCAATTAAACACA 57.020 25.926 0.00 0.00 0.00 3.72
45 46 9.686683 GGTCCATGATTTTACTATAGCCATATT 57.313 33.333 0.00 0.00 0.00 1.28
46 47 8.835734 TGGTCCATGATTTTACTATAGCCATAT 58.164 33.333 0.00 0.00 0.00 1.78
47 48 8.100791 GTGGTCCATGATTTTACTATAGCCATA 58.899 37.037 0.00 0.00 0.00 2.74
48 49 6.942576 GTGGTCCATGATTTTACTATAGCCAT 59.057 38.462 0.00 0.00 0.00 4.40
49 50 6.296026 GTGGTCCATGATTTTACTATAGCCA 58.704 40.000 0.00 0.00 0.00 4.75
50 51 5.705905 GGTGGTCCATGATTTTACTATAGCC 59.294 44.000 0.00 0.00 0.00 3.93
51 52 5.705905 GGGTGGTCCATGATTTTACTATAGC 59.294 44.000 0.00 0.00 35.00 2.97
52 53 7.079451 AGGGTGGTCCATGATTTTACTATAG 57.921 40.000 0.00 0.00 38.24 1.31
54 55 5.994416 AGGGTGGTCCATGATTTTACTAT 57.006 39.130 0.00 0.00 38.24 2.12
68 69 3.635869 TAGAGGGGCCAGGGTGGTC 62.636 68.421 4.39 0.00 42.67 4.02
69 70 3.622263 TAGAGGGGCCAGGGTGGT 61.622 66.667 4.39 0.00 40.46 4.16
70 71 2.770048 CTAGAGGGGCCAGGGTGG 60.770 72.222 4.39 0.00 41.55 4.61
71 72 2.605535 TAGCTAGAGGGGCCAGGGTG 62.606 65.000 4.39 0.00 0.00 4.61
72 73 1.679969 ATAGCTAGAGGGGCCAGGGT 61.680 60.000 4.39 0.00 0.00 4.34
73 74 0.413832 TATAGCTAGAGGGGCCAGGG 59.586 60.000 4.39 0.00 0.00 4.45
74 75 2.023501 AGATATAGCTAGAGGGGCCAGG 60.024 54.545 4.39 0.00 0.00 4.45
75 76 3.396685 AGATATAGCTAGAGGGGCCAG 57.603 52.381 4.39 0.00 0.00 4.85
76 77 5.162969 GGTATAGATATAGCTAGAGGGGCCA 60.163 48.000 4.39 0.00 34.68 5.36
77 78 5.075344 AGGTATAGATATAGCTAGAGGGGCC 59.925 48.000 9.30 0.00 43.09 5.80
78 79 6.208840 AGGTATAGATATAGCTAGAGGGGC 57.791 45.833 9.30 0.00 43.09 5.80
79 80 8.514533 AGTAGGTATAGATATAGCTAGAGGGG 57.485 42.308 15.62 0.00 44.91 4.79
379 438 4.277515 TGTCTCCAATCCTTGTTGAGAG 57.722 45.455 0.00 0.00 32.45 3.20
504 568 2.492088 GGCCCAAACAAAGATGGTCTAC 59.508 50.000 0.00 0.00 34.79 2.59
505 569 2.802719 GGCCCAAACAAAGATGGTCTA 58.197 47.619 0.00 0.00 34.79 2.59
602 667 0.391263 GACTAGCAAAGGGTCCGTGG 60.391 60.000 0.00 0.00 0.00 4.94
618 683 2.111972 TCCTCCTTCAACCAGTAGGACT 59.888 50.000 0.00 0.00 38.72 3.85
619 684 2.537143 TCCTCCTTCAACCAGTAGGAC 58.463 52.381 0.00 0.00 38.72 3.85
764 853 1.180029 GCCACTTGGAGTACGTAGGA 58.820 55.000 0.00 0.00 37.39 2.94
774 915 4.080356 ACAGCTAGATATTTGCCACTTGGA 60.080 41.667 0.00 0.00 37.39 3.53
875 1068 3.181478 CCTTACCGGTTTTAGCTCGATCT 60.181 47.826 15.04 0.00 0.00 2.75
905 1098 4.129737 TAGCTCGTGGCCTCGTGC 62.130 66.667 34.60 34.60 46.10 5.34
906 1099 2.103143 CTAGCTCGTGGCCTCGTG 59.897 66.667 25.10 23.17 43.05 4.35
907 1100 3.827898 GCTAGCTCGTGGCCTCGT 61.828 66.667 25.10 10.29 43.05 4.18
944 1142 1.081840 GTTGCCTTTGCGTGCTCTC 60.082 57.895 0.00 0.00 41.78 3.20
979 1178 1.521681 GTCGATCGGCCCCTTTCAG 60.522 63.158 16.41 0.00 0.00 3.02
1042 1243 3.712881 GAGCGCCACCACAACGAC 61.713 66.667 2.29 0.00 0.00 4.34
1109 1313 2.935481 TCTCCAGGTTGGGGCAGG 60.935 66.667 0.00 0.00 38.12 4.85
1232 1436 1.137675 CTCAATCGGCCAGTGATCAGA 59.862 52.381 2.24 0.00 0.00 3.27
1233 1437 1.579698 CTCAATCGGCCAGTGATCAG 58.420 55.000 2.24 0.00 0.00 2.90
1258 1462 5.312120 AGTCGACATGTAACTCTACAAGG 57.688 43.478 19.50 0.00 41.36 3.61
1267 1471 5.633601 TCAACTCATCAAGTCGACATGTAAC 59.366 40.000 19.50 0.00 37.17 2.50
1268 1472 5.778862 TCAACTCATCAAGTCGACATGTAA 58.221 37.500 19.50 1.07 37.17 2.41
1310 1514 1.725490 CAACGTACGTGCACAACAAG 58.275 50.000 23.57 6.23 0.00 3.16
1314 1518 1.639000 CTGCAACGTACGTGCACAA 59.361 52.632 28.98 16.22 34.61 3.33
1320 1524 2.357034 CAGCCCTGCAACGTACGT 60.357 61.111 16.72 16.72 0.00 3.57
1321 1525 2.357034 ACAGCCCTGCAACGTACG 60.357 61.111 15.01 15.01 0.00 3.67
1322 1526 1.301401 TCACAGCCCTGCAACGTAC 60.301 57.895 0.00 0.00 0.00 3.67
1323 1527 1.301401 GTCACAGCCCTGCAACGTA 60.301 57.895 0.00 0.00 0.00 3.57
1512 1716 1.740664 CTGGACGACGGACTCTCGA 60.741 63.158 0.00 0.00 35.08 4.04
1542 2101 1.794714 CCAGCTCCACCTGGTAGTAT 58.205 55.000 0.00 0.00 45.87 2.12
1659 2218 0.039764 TCATGTCGGTCTGGGAGAGT 59.960 55.000 0.00 0.00 0.00 3.24
1700 2259 6.315891 AGGAGAAGTTGATGAGTACGTACTAC 59.684 42.308 27.44 20.41 36.50 2.73
1703 2262 5.123502 TCAGGAGAAGTTGATGAGTACGTAC 59.876 44.000 18.10 18.10 0.00 3.67
1705 2264 4.079970 TCAGGAGAAGTTGATGAGTACGT 58.920 43.478 0.00 0.00 0.00 3.57
1706 2265 4.703645 TCAGGAGAAGTTGATGAGTACG 57.296 45.455 0.00 0.00 0.00 3.67
1713 2272 1.347707 TGGCGTTCAGGAGAAGTTGAT 59.652 47.619 0.00 0.00 33.63 2.57
1946 2519 3.170717 AGTAGGAGTTGTCGAATCCCAA 58.829 45.455 2.80 0.00 33.30 4.12
2038 2611 0.795735 CGTAGTAGTTGACGGTGCCG 60.796 60.000 9.29 9.29 46.03 5.69
2071 2644 3.438087 CGGTGAAGTCGTAGAAGAAGGTA 59.562 47.826 0.00 0.00 39.69 3.08
2192 2768 2.414658 TGAGCATCAGCAACCAGCCA 62.415 55.000 0.00 0.00 42.56 4.75
2319 2903 3.005554 CAGCCAAGGACATCTTACAGTG 58.994 50.000 0.00 0.00 33.68 3.66
2337 2921 1.945394 AGGCATCACAATTCGATCAGC 59.055 47.619 0.00 0.00 0.00 4.26
2439 3023 2.077627 GCTAGAGCCATCATCATGCTG 58.922 52.381 0.00 0.00 34.31 4.41
2475 3063 2.203084 TTTTGGTGCCAGTCGCGA 60.203 55.556 3.71 3.71 42.08 5.87
2706 4206 6.263617 AGGAGTAGTACAAAGGAAGATCGATC 59.736 42.308 17.91 17.91 0.00 3.69
2773 4273 3.181469 GGAGCCACGTATACTGAAATCCA 60.181 47.826 0.56 0.00 0.00 3.41
2775 4275 4.051922 CTGGAGCCACGTATACTGAAATC 58.948 47.826 0.56 0.00 0.00 2.17
2788 4288 0.033781 TTGCAAATTGCTGGAGCCAC 59.966 50.000 19.34 0.00 45.31 5.01
2789 4289 0.757512 TTTGCAAATTGCTGGAGCCA 59.242 45.000 19.34 0.00 45.31 4.75
2790 4290 1.881591 TTTTGCAAATTGCTGGAGCC 58.118 45.000 19.34 0.00 45.31 4.70
2791 4291 2.031769 GGTTTTTGCAAATTGCTGGAGC 60.032 45.455 19.34 8.27 45.31 4.70
2792 4292 3.469739 AGGTTTTTGCAAATTGCTGGAG 58.530 40.909 19.34 0.00 45.31 3.86
2793 4293 3.557228 AGGTTTTTGCAAATTGCTGGA 57.443 38.095 19.34 2.49 45.31 3.86
2796 4296 4.414337 TGGTAGGTTTTTGCAAATTGCT 57.586 36.364 19.34 0.00 45.31 3.91
2797 4297 5.491635 TTTGGTAGGTTTTTGCAAATTGC 57.508 34.783 13.65 11.58 45.29 3.56
2823 4323 5.752472 CCATGTATTTGTGAAAGCAAACACA 59.248 36.000 5.35 5.35 45.73 3.72
2824 4324 5.752955 ACCATGTATTTGTGAAAGCAAACAC 59.247 36.000 0.00 0.00 40.58 3.32
2826 4326 5.982516 TGACCATGTATTTGTGAAAGCAAAC 59.017 36.000 0.00 0.00 40.58 2.93
2862 4362 3.515602 AACAGGCAAGATCTTTCTGGT 57.484 42.857 26.50 21.92 30.72 4.00
2866 4366 5.392487 GCTAGGAAAACAGGCAAGATCTTTC 60.392 44.000 4.86 0.00 0.00 2.62
2889 4389 4.125703 CCTTAGACATCACCAAGATCTGC 58.874 47.826 0.00 0.00 33.72 4.26
2995 4502 0.403271 ACCTCCAGCTTGTCATGCTT 59.597 50.000 10.38 0.00 38.92 3.91
3009 4516 4.944372 CGGTATCGCGCCACCTCC 62.944 72.222 21.60 9.14 32.29 4.30
3048 4555 1.134401 TCCATCTCAATCCAACCTCGC 60.134 52.381 0.00 0.00 0.00 5.03
3099 4606 8.798975 AATCTTTAGATCTACACCCTATGGAA 57.201 34.615 0.67 0.00 32.75 3.53
3100 4607 8.651389 CAAATCTTTAGATCTACACCCTATGGA 58.349 37.037 0.67 0.00 32.75 3.41
3101 4608 7.880195 CCAAATCTTTAGATCTACACCCTATGG 59.120 40.741 0.67 2.96 32.75 2.74
3102 4609 8.651389 TCCAAATCTTTAGATCTACACCCTATG 58.349 37.037 0.67 0.00 32.75 2.23
3120 4631 5.975693 TTGCGGAGTTATTTTCCAAATCT 57.024 34.783 0.00 0.00 34.24 2.40


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

AutoCloner maintained by Alex Coulton.