Multiple sequence alignment - TraesCS3D01G207100

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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 TraesCS3D01G207100 chr3D 100.000 2954 0 0 1 2954 272091168 272088215 0.000000e+00 5456
1 TraesCS3D01G207100 chr3D 95.123 2235 76 12 744 2954 247888492 247886267 0.000000e+00 3493
2 TraesCS3D01G207100 chr3D 88.560 778 46 24 1 739 152827214 152827987 0.000000e+00 904
3 TraesCS3D01G207100 chr3D 88.183 787 45 20 1 748 247889314 247888537 0.000000e+00 894
4 TraesCS3D01G207100 chr7A 95.089 2240 78 10 738 2954 176257308 176259538 0.000000e+00 3498
5 TraesCS3D01G207100 chr5A 94.929 2248 82 9 730 2954 422074650 422072412 0.000000e+00 3491
6 TraesCS3D01G207100 chr5A 94.598 2240 86 8 738 2954 489874254 489876481 0.000000e+00 3434
7 TraesCS3D01G207100 chr5A 87.130 777 59 24 1 739 489873430 489874203 0.000000e+00 843
8 TraesCS3D01G207100 chr2A 95.000 2240 80 7 738 2954 642923953 642921723 0.000000e+00 3487
9 TraesCS3D01G207100 chr2A 94.821 2240 84 6 738 2954 351420340 351422570 0.000000e+00 3465
10 TraesCS3D01G207100 chr2A 94.441 1601 57 6 1377 2954 351178305 351176714 0.000000e+00 2435
11 TraesCS3D01G207100 chr2A 88.327 771 49 23 1 733 233461341 233462108 0.000000e+00 887
12 TraesCS3D01G207100 chr2A 86.250 560 38 24 1 528 588277280 588276728 3.300000e-159 571
13 TraesCS3D01G207100 chr4A 94.911 2240 82 9 738 2954 548525458 548523228 0.000000e+00 3476
14 TraesCS3D01G207100 chr6B 94.911 2240 81 8 738 2954 325035109 325037338 0.000000e+00 3474
15 TraesCS3D01G207100 chr6B 94.288 2241 83 13 738 2954 458496474 458498693 0.000000e+00 3387
16 TraesCS3D01G207100 chr4B 94.911 2240 81 11 738 2954 439196268 439198497 0.000000e+00 3474
17 TraesCS3D01G207100 chr4B 94.554 2240 89 7 738 2954 165292225 165294454 0.000000e+00 3430
18 TraesCS3D01G207100 chr4B 92.171 281 20 2 1 279 165291398 165291678 2.130000e-106 396
19 TraesCS3D01G207100 chr4B 98.193 166 3 0 2789 2954 285536874 285536709 1.040000e-74 291
20 TraesCS3D01G207100 chr6A 94.866 2240 83 12 738 2954 466092980 466095210 0.000000e+00 3470
21 TraesCS3D01G207100 chr6A 94.433 1401 45 8 1577 2954 297636584 297635194 0.000000e+00 2124
22 TraesCS3D01G207100 chr6A 88.946 778 52 18 6 750 6598221 6598997 0.000000e+00 929
23 TraesCS3D01G207100 chr6A 87.802 787 54 23 1 748 297637755 297636972 0.000000e+00 883
24 TraesCS3D01G207100 chr1A 94.866 2240 83 9 738 2954 80308133 80305903 0.000000e+00 3470
25 TraesCS3D01G207100 chr2B 94.866 2240 82 7 738 2954 669227546 669229775 0.000000e+00 3469
26 TraesCS3D01G207100 chr5B 94.866 2240 78 9 738 2954 146820108 146817883 0.000000e+00 3465
27 TraesCS3D01G207100 chr5B 94.777 2240 85 6 738 2954 161075592 161077822 0.000000e+00 3459
28 TraesCS3D01G207100 chr5B 93.910 936 30 5 2037 2954 208431541 208432467 0.000000e+00 1387
29 TraesCS3D01G207100 chr5B 91.393 488 28 8 271 750 146820626 146820145 0.000000e+00 656
30 TraesCS3D01G207100 chr5B 93.238 281 17 2 1 279 146820928 146820648 2.120000e-111 412
31 TraesCS3D01G207100 chr1B 94.509 2240 90 7 738 2954 539560623 539558394 0.000000e+00 3424
32 TraesCS3D01G207100 chrUn 94.018 1237 42 6 1741 2954 401101034 401102261 0.000000e+00 1845
33 TraesCS3D01G207100 chrUn 92.460 504 11 6 2469 2954 449426717 449426223 0.000000e+00 695
34 TraesCS3D01G207100 chrUn 89.959 488 38 5 271 748 436873198 436872712 1.160000e-173 619
35 TraesCS3D01G207100 chr3B 87.836 781 52 18 1 739 548843177 548843956 0.000000e+00 876


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 TraesCS3D01G207100 chr3D 272088215 272091168 2953 True 5456.0 5456 100.000000 1 2954 1 chr3D.!!$R1 2953
1 TraesCS3D01G207100 chr3D 247886267 247889314 3047 True 2193.5 3493 91.653000 1 2954 2 chr3D.!!$R2 2953
2 TraesCS3D01G207100 chr3D 152827214 152827987 773 False 904.0 904 88.560000 1 739 1 chr3D.!!$F1 738
3 TraesCS3D01G207100 chr7A 176257308 176259538 2230 False 3498.0 3498 95.089000 738 2954 1 chr7A.!!$F1 2216
4 TraesCS3D01G207100 chr5A 422072412 422074650 2238 True 3491.0 3491 94.929000 730 2954 1 chr5A.!!$R1 2224
5 TraesCS3D01G207100 chr5A 489873430 489876481 3051 False 2138.5 3434 90.864000 1 2954 2 chr5A.!!$F1 2953
6 TraesCS3D01G207100 chr2A 642921723 642923953 2230 True 3487.0 3487 95.000000 738 2954 1 chr2A.!!$R3 2216
7 TraesCS3D01G207100 chr2A 351420340 351422570 2230 False 3465.0 3465 94.821000 738 2954 1 chr2A.!!$F2 2216
8 TraesCS3D01G207100 chr2A 351176714 351178305 1591 True 2435.0 2435 94.441000 1377 2954 1 chr2A.!!$R1 1577
9 TraesCS3D01G207100 chr2A 233461341 233462108 767 False 887.0 887 88.327000 1 733 1 chr2A.!!$F1 732
10 TraesCS3D01G207100 chr2A 588276728 588277280 552 True 571.0 571 86.250000 1 528 1 chr2A.!!$R2 527
11 TraesCS3D01G207100 chr4A 548523228 548525458 2230 True 3476.0 3476 94.911000 738 2954 1 chr4A.!!$R1 2216
12 TraesCS3D01G207100 chr6B 325035109 325037338 2229 False 3474.0 3474 94.911000 738 2954 1 chr6B.!!$F1 2216
13 TraesCS3D01G207100 chr6B 458496474 458498693 2219 False 3387.0 3387 94.288000 738 2954 1 chr6B.!!$F2 2216
14 TraesCS3D01G207100 chr4B 439196268 439198497 2229 False 3474.0 3474 94.911000 738 2954 1 chr4B.!!$F1 2216
15 TraesCS3D01G207100 chr4B 165291398 165294454 3056 False 1913.0 3430 93.362500 1 2954 2 chr4B.!!$F2 2953
16 TraesCS3D01G207100 chr6A 466092980 466095210 2230 False 3470.0 3470 94.866000 738 2954 1 chr6A.!!$F2 2216
17 TraesCS3D01G207100 chr6A 297635194 297637755 2561 True 1503.5 2124 91.117500 1 2954 2 chr6A.!!$R1 2953
18 TraesCS3D01G207100 chr6A 6598221 6598997 776 False 929.0 929 88.946000 6 750 1 chr6A.!!$F1 744
19 TraesCS3D01G207100 chr1A 80305903 80308133 2230 True 3470.0 3470 94.866000 738 2954 1 chr1A.!!$R1 2216
20 TraesCS3D01G207100 chr2B 669227546 669229775 2229 False 3469.0 3469 94.866000 738 2954 1 chr2B.!!$F1 2216
21 TraesCS3D01G207100 chr5B 161075592 161077822 2230 False 3459.0 3459 94.777000 738 2954 1 chr5B.!!$F1 2216
22 TraesCS3D01G207100 chr5B 146817883 146820928 3045 True 1511.0 3465 93.165667 1 2954 3 chr5B.!!$R1 2953
23 TraesCS3D01G207100 chr5B 208431541 208432467 926 False 1387.0 1387 93.910000 2037 2954 1 chr5B.!!$F2 917
24 TraesCS3D01G207100 chr1B 539558394 539560623 2229 True 3424.0 3424 94.509000 738 2954 1 chr1B.!!$R1 2216
25 TraesCS3D01G207100 chrUn 401101034 401102261 1227 False 1845.0 1845 94.018000 1741 2954 1 chrUn.!!$F1 1213
26 TraesCS3D01G207100 chr3B 548843177 548843956 779 False 876.0 876 87.836000 1 739 1 chr3B.!!$F1 738

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
353 389 0.396435 TCCTCTTTTCCTGCTTCGCA 59.604 50.0 0.0 0.0 36.92 5.10 F
1000 1100 0.034337 GCACCGTTGTAGAACCAGGA 59.966 55.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1874 0.178975 TTTGCCTTTGGACGTCCCAT 60.179 50.0 31.19 0.0 46.1 4.00 R
2701 2811 0.324091 AGCCATGAGAGCCCCAAAAG 60.324 55.0 0.00 0.0 0.0 2.27 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
91 94 3.316573 CTCTTCCCCTGTCCCGTGC 62.317 68.421 0.00 0.00 0.00 5.34
92 95 3.636231 CTTCCCCTGTCCCGTGCA 61.636 66.667 0.00 0.00 0.00 4.57
130 133 2.591715 ACACTCACGCAGGCAACC 60.592 61.111 0.00 0.00 37.17 3.77
135 138 3.716006 CACGCAGGCAACCAGACG 61.716 66.667 0.00 0.00 37.17 4.18
155 159 3.672295 GAAGGGAGGCGCTGTCTGG 62.672 68.421 7.64 0.00 0.00 3.86
194 199 2.107366 TCAACATGGTATCGAGCCAGA 58.893 47.619 15.33 6.15 39.65 3.86
204 209 3.429141 GAGCCAGACGACGACGGA 61.429 66.667 12.58 0.00 44.46 4.69
279 315 4.008933 GAGGAGGCTGGTGCGTGT 62.009 66.667 0.00 0.00 40.82 4.49
341 377 1.352687 GGAGGGAACTGCTTCCTCTTT 59.647 52.381 5.41 0.00 46.74 2.52
353 389 0.396435 TCCTCTTTTCCTGCTTCGCA 59.604 50.000 0.00 0.00 36.92 5.10
435 474 2.046892 TGCAGCGGGAAGAAGAGC 60.047 61.111 0.00 0.00 0.00 4.09
600 642 3.198236 TTGTGCGGCTGCTTCTTGC 62.198 57.895 20.27 2.74 43.34 4.01
625 667 0.898320 CGGCAGAGGAAGAAAGAGGA 59.102 55.000 0.00 0.00 0.00 3.71
733 779 1.102809 TGCTGTTGTGAGCTTGGTGG 61.103 55.000 0.00 0.00 39.90 4.61
736 782 0.751277 TGTTGTGAGCTTGGTGGTGG 60.751 55.000 0.00 0.00 0.00 4.61
742 842 3.982241 GCTTGGTGGTGGTGCTGC 61.982 66.667 0.00 0.00 0.00 5.25
796 896 1.028868 ATGCTCTTGCCGAGGCTTTC 61.029 55.000 15.75 1.28 40.25 2.62
829 929 1.066587 GATCCTCGCGGAGTCCAAG 59.933 63.158 10.49 1.97 44.06 3.61
842 942 1.541118 TCCAAGTCTGGGGCCATCA 60.541 57.895 4.39 0.61 43.71 3.07
886 986 0.678048 AGCTTGAAATGTCGCCCCTC 60.678 55.000 0.00 0.00 0.00 4.30
907 1007 1.348775 ACATGAAGCTAGAGGGGGCC 61.349 60.000 0.00 0.00 0.00 5.80
925 1025 3.195396 GGGCCACAAATTATTTGAGCTGA 59.805 43.478 22.53 0.00 43.26 4.26
928 1028 5.163478 GGCCACAAATTATTTGAGCTGATCT 60.163 40.000 22.53 0.00 43.26 2.75
1000 1100 0.034337 GCACCGTTGTAGAACCAGGA 59.966 55.000 0.00 0.00 0.00 3.86
1112 1212 0.399091 CTCTGTGGAGGGGCTATCCA 60.399 60.000 7.06 7.06 44.63 3.41
1129 1229 2.470990 TCCACACCTGCTGAGATATGT 58.529 47.619 0.00 0.00 0.00 2.29
1144 1244 7.055667 TGAGATATGTAAGATTCTGTCCACC 57.944 40.000 0.00 0.00 0.00 4.61
1205 1305 6.013379 TCAGATTGAGGACAAGATTAGGTTGT 60.013 38.462 0.00 0.00 40.89 3.32
1236 1336 3.353370 TGATGGCATGTCAGTGATGAA 57.647 42.857 3.81 0.00 0.00 2.57
1327 1428 1.363744 CTTCAATCGAGTCAGGGCAC 58.636 55.000 0.00 0.00 0.00 5.01
1482 1583 2.203209 GGTGCGCCTATCCCTTGG 60.203 66.667 9.68 0.00 0.00 3.61
1522 1623 1.153958 GCCAGCTTCGACATTTGCC 60.154 57.895 0.00 0.00 0.00 4.52
1608 1709 3.903714 TGGAAGAGAGAATGTCCAACTCA 59.096 43.478 0.00 0.00 37.22 3.41
1649 1750 1.151810 AGAGGGGGAACAGGCAGAA 60.152 57.895 0.00 0.00 0.00 3.02
1651 1752 2.361737 GGGGGAACAGGCAGAAGC 60.362 66.667 0.00 0.00 41.10 3.86
1653 1754 1.000396 GGGGAACAGGCAGAAGCAT 60.000 57.895 0.00 0.00 44.61 3.79
1680 1781 4.168283 TGCTAGAGGTAGAGGTGGATACTT 59.832 45.833 0.00 0.00 37.61 2.24
1684 1785 6.593759 AGAGGTAGAGGTGGATACTTAGAA 57.406 41.667 0.00 0.00 37.61 2.10
1773 1874 2.281484 GGCCGTTGCAGGAGACAA 60.281 61.111 0.00 0.00 40.13 3.18
1842 1943 1.965754 GCTCACTGGGCCTCCACTAG 61.966 65.000 4.53 0.00 38.32 2.57
1883 1989 4.098654 TCTCTTGCTACTAATGAGAGTGCC 59.901 45.833 0.00 0.00 36.22 5.01
1937 2043 2.352960 GCATGTTGCTAGTAACTCCTGC 59.647 50.000 22.00 21.32 40.96 4.85
1954 2060 2.390938 CTGCGTGTTCGAGTCTTACAA 58.609 47.619 0.00 0.00 39.71 2.41
1976 2082 0.252421 AGCATCCTCCCTCTCACACA 60.252 55.000 0.00 0.00 0.00 3.72
2086 2192 1.164411 TTACATGTGCCAGCCTTTCG 58.836 50.000 9.11 0.00 0.00 3.46
2102 2208 3.563808 CCTTTCGTGTCAATTTGGTCTCA 59.436 43.478 0.00 0.00 0.00 3.27
2107 2213 4.819088 TCGTGTCAATTTGGTCTCATTCAA 59.181 37.500 0.00 0.00 0.00 2.69
2108 2214 4.911610 CGTGTCAATTTGGTCTCATTCAAC 59.088 41.667 0.00 0.00 0.00 3.18
2132 2238 4.439700 GCACTCATTGATCAAATGGACTGG 60.440 45.833 13.09 2.50 45.00 4.00
2135 2241 0.810648 TTGATCAAATGGACTGGCGC 59.189 50.000 5.45 0.00 0.00 6.53
2155 2261 1.126846 CGTGATCCTTGACAAGTTCGC 59.873 52.381 14.03 14.28 0.00 4.70
2167 2273 3.549299 CAAGTTCGCTTGCTTGATTCT 57.451 42.857 5.45 0.00 46.63 2.40
2180 2286 0.678950 TGATTCTGGTGCGACAGACA 59.321 50.000 9.40 3.73 46.44 3.41
2330 2436 3.319122 GGATGGGGCATGTATCTTTTGAC 59.681 47.826 0.00 0.00 0.00 3.18
2382 2488 2.171003 GTGGAATAGGCAAAGGCAAGT 58.829 47.619 0.00 0.00 43.71 3.16
2399 2505 2.984471 CAAGTTGACATGTGATGCTTGC 59.016 45.455 1.15 0.00 0.00 4.01
2420 2526 3.804688 CGAATATGCAAAACACACACGA 58.195 40.909 0.00 0.00 0.00 4.35
2544 2654 9.297037 AGTATTTTGCTACCTTTATTGACTGTT 57.703 29.630 0.00 0.00 0.00 3.16
2547 2657 8.685838 TTTTGCTACCTTTATTGACTGTTAGT 57.314 30.769 0.00 0.00 0.00 2.24
2548 2658 7.900782 TTGCTACCTTTATTGACTGTTAGTC 57.099 36.000 2.11 2.11 45.26 2.59
2549 2659 7.241042 TGCTACCTTTATTGACTGTTAGTCT 57.759 36.000 10.03 0.00 45.27 3.24
2550 2660 7.097192 TGCTACCTTTATTGACTGTTAGTCTG 58.903 38.462 10.03 0.00 45.27 3.51
2551 2661 7.097834 GCTACCTTTATTGACTGTTAGTCTGT 58.902 38.462 10.03 2.27 45.27 3.41
2614 2724 5.009610 GGATGAGGTGTTTAGCTGTTTTCAA 59.990 40.000 0.00 0.00 34.13 2.69
2615 2725 5.906113 TGAGGTGTTTAGCTGTTTTCAAA 57.094 34.783 0.00 0.00 34.13 2.69
2651 2761 5.828299 TTGTAAAGAACCAGTTTCAGGTG 57.172 39.130 0.00 0.00 39.86 4.00
2701 2811 3.185797 GGAACGGAGTATGTGAACAACAC 59.814 47.826 0.00 0.00 45.00 3.32
2712 2822 1.754226 TGAACAACACTTTTGGGGCTC 59.246 47.619 0.00 0.00 0.00 4.70
2778 2890 0.916358 CCCCCTCAGAATGGAGTGGT 60.916 60.000 0.00 0.00 36.16 4.16
2875 3004 3.244875 ACAGCCACATACTTGATCAACCA 60.245 43.478 3.38 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 94 1.078918 TCTCAGATGTGGCGGCTTG 60.079 57.895 11.43 1.23 0.00 4.01
92 95 1.078848 GTCTCAGATGTGGCGGCTT 60.079 57.895 11.43 0.00 0.00 4.35
130 133 4.148825 CGCCTCCCTTCCCGTCTG 62.149 72.222 0.00 0.00 0.00 3.51
135 138 4.475135 GACAGCGCCTCCCTTCCC 62.475 72.222 2.29 0.00 0.00 3.97
262 267 4.008933 ACACGCACCAGCCTCCTC 62.009 66.667 0.00 0.00 37.52 3.71
328 364 1.423161 AGCAGGAAAAGAGGAAGCAGT 59.577 47.619 0.00 0.00 0.00 4.40
353 389 2.774351 GCTAGCCACCCCAGGGAT 60.774 66.667 7.25 0.00 38.96 3.85
375 411 3.522731 CTCCTCGGACGCCTCCTG 61.523 72.222 0.07 0.00 33.79 3.86
421 457 1.610673 TCCTGCTCTTCTTCCCGCT 60.611 57.895 0.00 0.00 0.00 5.52
435 474 2.124942 GCCGCCTTCTTCCTCCTG 60.125 66.667 0.00 0.00 0.00 3.86
505 544 0.034476 CTCCTCTGTTCAGCAGCACA 59.966 55.000 0.00 0.00 44.66 4.57
537 576 0.459489 GGAACAACACAAGGCAGCAA 59.541 50.000 0.00 0.00 0.00 3.91
578 620 3.606065 GAAGCAGCCGCACAAGCAG 62.606 63.158 0.00 0.00 42.27 4.24
670 712 0.938713 TAAAGCACACAAACGGTCCG 59.061 50.000 10.48 10.48 0.00 4.79
733 779 1.310933 ATAAGCAGCAGCAGCACCAC 61.311 55.000 12.92 0.00 45.49 4.16
736 782 1.722636 GGGATAAGCAGCAGCAGCAC 61.723 60.000 12.92 0.00 45.49 4.40
742 842 1.031571 TTTGGCGGGATAAGCAGCAG 61.032 55.000 0.00 0.00 36.08 4.24
777 877 1.001641 AAAGCCTCGGCAAGAGCAT 60.002 52.632 11.02 0.00 45.54 3.79
780 880 3.479370 CGAAAGCCTCGGCAAGAG 58.521 61.111 11.02 1.85 44.20 2.85
829 929 0.179006 GAGGAATGATGGCCCCAGAC 60.179 60.000 0.00 0.00 0.00 3.51
886 986 0.390860 CCCCCTCTAGCTTCATGTCG 59.609 60.000 0.00 0.00 0.00 4.35
907 1007 8.442632 TCCTAGATCAGCTCAAATAATTTGTG 57.557 34.615 0.00 0.00 41.36 3.33
925 1025 1.216990 CCCACAAAGCCCTCCTAGAT 58.783 55.000 0.00 0.00 0.00 1.98
928 1028 1.541368 AGCCCACAAAGCCCTCCTA 60.541 57.895 0.00 0.00 0.00 2.94
1000 1100 2.175202 CCCTCTGCACTACTCTTGTCT 58.825 52.381 0.00 0.00 0.00 3.41
1112 1212 6.326064 AGAATCTTACATATCTCAGCAGGTGT 59.674 38.462 0.00 0.00 0.00 4.16
1129 1229 5.964477 AGAGTATTGGGTGGACAGAATCTTA 59.036 40.000 0.00 0.00 0.00 2.10
1144 1244 0.034186 TGCCCTTGCCAGAGTATTGG 60.034 55.000 0.00 0.00 41.35 3.16
1236 1336 1.442769 CTGCAGTTCTGCCACGTATT 58.557 50.000 19.91 0.00 0.00 1.89
1327 1428 2.693762 CCTGCGTGCCATCCACTTG 61.694 63.158 0.00 0.00 42.42 3.16
1482 1583 1.135199 CAACCTTCACATCTGCATGCC 60.135 52.381 16.68 0.00 32.57 4.40
1522 1623 2.125952 TCCATGCGCTCAGTGACG 60.126 61.111 9.73 9.77 0.00 4.35
1608 1709 0.477202 ATATCCCCTGCCTCTGCCAT 60.477 55.000 0.00 0.00 36.33 4.40
1651 1752 4.279671 CCACCTCTACCTCTAGCACTTATG 59.720 50.000 0.00 0.00 0.00 1.90
1653 1754 3.526430 TCCACCTCTACCTCTAGCACTTA 59.474 47.826 0.00 0.00 0.00 2.24
1680 1781 0.918983 CTGGCCCCATGAGGTTTCTA 59.081 55.000 0.00 0.00 0.00 2.10
1684 1785 4.066139 GCCTGGCCCCATGAGGTT 62.066 66.667 7.66 0.00 0.00 3.50
1773 1874 0.178975 TTTGCCTTTGGACGTCCCAT 60.179 50.000 31.19 0.00 46.10 4.00
1842 1943 0.665298 GATGCTCTTTCCGGATTGCC 59.335 55.000 4.15 0.00 0.00 4.52
1843 1944 1.601430 GAGATGCTCTTTCCGGATTGC 59.399 52.381 4.15 8.27 0.00 3.56
1844 1945 3.191078 AGAGATGCTCTTTCCGGATTG 57.809 47.619 4.15 0.58 37.60 2.67
1937 2043 4.619760 TGCTTATTGTAAGACTCGAACACG 59.380 41.667 1.10 0.00 0.00 4.49
1954 2060 2.703007 GTGTGAGAGGGAGGATGCTTAT 59.297 50.000 0.00 0.00 0.00 1.73
1976 2082 1.553248 TCAGCCGTTTGTATAGTGCCT 59.447 47.619 0.00 0.00 0.00 4.75
2043 2149 2.361119 CTGACGATAGGGAAATGGTCGA 59.639 50.000 0.00 0.00 37.40 4.20
2086 2192 4.911610 CGTTGAATGAGACCAAATTGACAC 59.088 41.667 0.00 0.00 0.00 3.67
2107 2213 3.127548 GTCCATTTGATCAATGAGTGCGT 59.872 43.478 9.40 0.00 44.78 5.24
2108 2214 3.376234 AGTCCATTTGATCAATGAGTGCG 59.624 43.478 9.40 2.12 44.78 5.34
2132 2238 1.291877 ACTTGTCAAGGATCACGCGC 61.292 55.000 16.85 0.00 0.00 6.86
2135 2241 1.126846 GCGAACTTGTCAAGGATCACG 59.873 52.381 16.85 13.70 0.00 4.35
2155 2261 1.135859 GTCGCACCAGAATCAAGCAAG 60.136 52.381 0.00 0.00 0.00 4.01
2167 2273 2.280797 GGCTTGTCTGTCGCACCA 60.281 61.111 0.00 0.00 0.00 4.17
2180 2286 2.147387 AGTCCCAACCGTCTGGCTT 61.147 57.895 0.00 0.00 39.70 4.35
2211 2317 2.505982 CATGTACCAGAGCCCCCG 59.494 66.667 0.00 0.00 0.00 5.73
2330 2436 7.875041 ACATCCGGAAATATTCTACTCATCTTG 59.125 37.037 9.01 0.00 0.00 3.02
2382 2488 1.521580 TCGCAAGCATCACATGTCAA 58.478 45.000 0.00 0.00 37.18 3.18
2399 2505 3.804688 TCGTGTGTGTTTTGCATATTCG 58.195 40.909 0.00 0.00 0.00 3.34
2544 2654 5.836821 AGTCATGCGAGAATAACAGACTA 57.163 39.130 0.00 0.00 33.72 2.59
2545 2655 4.727507 AGTCATGCGAGAATAACAGACT 57.272 40.909 0.00 0.00 0.00 3.24
2546 2656 4.033358 CCAAGTCATGCGAGAATAACAGAC 59.967 45.833 0.00 0.00 0.00 3.51
2547 2657 4.081697 TCCAAGTCATGCGAGAATAACAGA 60.082 41.667 0.00 0.00 0.00 3.41
2548 2658 4.183865 TCCAAGTCATGCGAGAATAACAG 58.816 43.478 0.00 0.00 0.00 3.16
2549 2659 4.200838 TCCAAGTCATGCGAGAATAACA 57.799 40.909 0.00 0.00 0.00 2.41
2550 2660 5.741388 AATCCAAGTCATGCGAGAATAAC 57.259 39.130 0.00 0.00 0.00 1.89
2551 2661 7.047891 AGTAAATCCAAGTCATGCGAGAATAA 58.952 34.615 0.00 0.00 0.00 1.40
2614 2724 6.959639 TCTTTACAAGAGCATGGAAGTTTT 57.040 33.333 0.00 0.00 32.71 2.43
2615 2725 6.239036 GGTTCTTTACAAGAGCATGGAAGTTT 60.239 38.462 0.00 0.00 40.12 2.66
2651 2761 1.673665 CCTGAGCACCTTGACCTGC 60.674 63.158 0.00 0.00 0.00 4.85
2701 2811 0.324091 AGCCATGAGAGCCCCAAAAG 60.324 55.000 0.00 0.00 0.00 2.27
2778 2890 1.585006 GAGCAACCTCTCCGTTCGA 59.415 57.895 0.00 0.00 35.16 3.71
2875 3004 3.707102 GCCAAGTATCCTAGAAGGTGTCT 59.293 47.826 0.00 0.00 40.71 3.41


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

AutoCloner maintained by Alex Coulton.