Multiple sequence alignment - TraesCS3D01G116800

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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 TraesCS3D01G116800 chr3D 100.000 3608 0 0 1 3608 70247842 70244235 0.000000e+00 6663
1 TraesCS3D01G116800 chr3D 91.986 287 23 0 66 352 582180523 582180809 1.560000e-108 403
2 TraesCS3D01G116800 chr3D 80.653 429 49 19 559 963 70274506 70274088 5.850000e-78 302
3 TraesCS3D01G116800 chr3D 87.831 189 23 0 376 564 70274726 70274538 4.690000e-54 222
4 TraesCS3D01G116800 chr3D 95.833 72 3 0 1 72 582180268 582180339 2.280000e-22 117
5 TraesCS3D01G116800 chr3B 91.341 3303 185 44 381 3608 116113482 116110206 0.000000e+00 4421
6 TraesCS3D01G116800 chr3A 94.208 1036 51 5 1573 2601 81696272 81695239 0.000000e+00 1572
7 TraesCS3D01G116800 chr3A 92.205 821 38 5 2814 3608 81695243 81694423 0.000000e+00 1138
8 TraesCS3D01G116800 chr3A 92.848 797 33 10 745 1529 81697060 81696276 0.000000e+00 1134
9 TraesCS3D01G116800 chr2A 95.751 353 15 0 1 353 655743210 655743562 1.450000e-158 569
10 TraesCS3D01G116800 chr5A 94.334 353 20 0 1 353 457837750 457837398 3.170000e-150 542
11 TraesCS3D01G116800 chr5D 89.266 354 34 4 1 352 202679748 202680099 1.190000e-119 440
12 TraesCS3D01G116800 chr1B 77.864 646 120 20 1674 2311 677914542 677913912 2.630000e-101 379
13 TraesCS3D01G116800 chr1A 86.301 292 40 0 1674 1965 584374460 584374169 5.810000e-83 318
14 TraesCS3D01G116800 chr2D 80.342 351 69 0 2 352 414408342 414408692 2.140000e-67 267


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 TraesCS3D01G116800 chr3D 70244235 70247842 3607 True 6663.000000 6663 100.0000 1 3608 1 chr3D.!!$R1 3607
1 TraesCS3D01G116800 chr3D 70274088 70274726 638 True 262.000000 302 84.2420 376 963 2 chr3D.!!$R2 587
2 TraesCS3D01G116800 chr3D 582180268 582180809 541 False 260.000000 403 93.9095 1 352 2 chr3D.!!$F1 351
3 TraesCS3D01G116800 chr3B 116110206 116113482 3276 True 4421.000000 4421 91.3410 381 3608 1 chr3B.!!$R1 3227
4 TraesCS3D01G116800 chr3A 81694423 81697060 2637 True 1281.333333 1572 93.0870 745 3608 3 chr3A.!!$R1 2863
5 TraesCS3D01G116800 chr1B 677913912 677914542 630 True 379.000000 379 77.8640 1674 2311 1 chr1B.!!$R1 637

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
161 352 0.039074 CGCCGAGTAAGCCATAGAGG 60.039 60.0 0.00 0.0 41.84 3.69 F
244 435 0.102481 GCCTCAAATGCATGAGCTGG 59.898 55.0 11.19 6.7 44.43 4.85 F
1515 1766 0.107508 CCTCGTCCTCACCGGTAGTA 60.108 60.0 6.87 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2080 0.462759 CGTCCAGGATCTTGCCCTTC 60.463 60.0 0.00 0.0 0.00 3.46 R
2183 2452 0.032515 TATCGGAGAAGCCCTGGACA 60.033 55.0 0.00 0.0 43.58 4.02 R
3164 3476 0.161446 GTTGCGGCATTTTCTTTGCG 59.839 50.0 2.28 0.0 41.07 4.85 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
89 280 1.676529 CAATGCTTCTCCAGATGGCTG 59.323 52.381 0.00 0.00 41.93 4.85
112 303 1.295423 GTAAGGGCAACTCGGCAGA 59.705 57.895 0.00 0.00 43.60 4.26
126 317 0.951040 GGCAGACCCTCACAAAGACG 60.951 60.000 0.00 0.00 0.00 4.18
151 342 3.446507 GGTGGATTTCGCCGAGTAA 57.553 52.632 0.00 0.00 36.17 2.24
157 348 2.547218 GGATTTCGCCGAGTAAGCCATA 60.547 50.000 1.18 0.00 35.99 2.74
161 352 0.039074 CGCCGAGTAAGCCATAGAGG 60.039 60.000 0.00 0.00 41.84 3.69
163 354 1.896465 GCCGAGTAAGCCATAGAGGAT 59.104 52.381 0.00 0.00 41.22 3.24
190 381 1.680338 GCCACAGAAAACTGTCAGGT 58.320 50.000 4.53 0.00 35.03 4.00
192 383 2.917933 CCACAGAAAACTGTCAGGTGA 58.082 47.619 4.53 0.00 35.03 4.02
194 385 2.614057 CACAGAAAACTGTCAGGTGACC 59.386 50.000 7.64 0.00 44.15 4.02
244 435 0.102481 GCCTCAAATGCATGAGCTGG 59.898 55.000 11.19 6.70 44.43 4.85
259 450 1.842562 AGCTGGATAAGAGCCATGTGT 59.157 47.619 0.00 0.00 37.12 3.72
262 453 3.877559 CTGGATAAGAGCCATGTGTGAA 58.122 45.455 0.00 0.00 34.33 3.18
265 456 4.019411 TGGATAAGAGCCATGTGTGAAGAA 60.019 41.667 0.00 0.00 0.00 2.52
277 468 4.081406 TGTGTGAAGAAATGAAGGGGATG 58.919 43.478 0.00 0.00 0.00 3.51
283 474 2.922283 AGAAATGAAGGGGATGTCCAGT 59.078 45.455 0.86 0.00 37.91 4.00
289 480 0.475632 AGGGGATGTCCAGTGACCAA 60.476 55.000 0.86 0.00 41.01 3.67
300 491 0.908198 AGTGACCAATGCTCCTCCTC 59.092 55.000 0.00 0.00 0.00 3.71
337 528 3.049674 CTGGTGTTGATGCGGCGT 61.050 61.111 9.37 0.00 0.00 5.68
352 543 1.080772 GCGTGTGTCGACCATCTCA 60.081 57.895 14.12 1.96 42.86 3.27
353 544 0.458543 GCGTGTGTCGACCATCTCAT 60.459 55.000 14.12 0.00 42.86 2.90
354 545 1.996292 CGTGTGTCGACCATCTCATT 58.004 50.000 14.12 0.00 42.86 2.57
355 546 2.337583 CGTGTGTCGACCATCTCATTT 58.662 47.619 14.12 0.00 42.86 2.32
356 547 2.345641 CGTGTGTCGACCATCTCATTTC 59.654 50.000 14.12 0.00 42.86 2.17
357 548 2.673368 GTGTGTCGACCATCTCATTTCC 59.327 50.000 14.12 0.00 0.00 3.13
358 549 2.567169 TGTGTCGACCATCTCATTTCCT 59.433 45.455 14.12 0.00 0.00 3.36
359 550 3.007940 TGTGTCGACCATCTCATTTCCTT 59.992 43.478 14.12 0.00 0.00 3.36
360 551 4.003648 GTGTCGACCATCTCATTTCCTTT 58.996 43.478 14.12 0.00 0.00 3.11
361 552 4.093556 GTGTCGACCATCTCATTTCCTTTC 59.906 45.833 14.12 0.00 0.00 2.62
362 553 3.623510 GTCGACCATCTCATTTCCTTTCC 59.376 47.826 3.51 0.00 0.00 3.13
363 554 3.263170 TCGACCATCTCATTTCCTTTCCA 59.737 43.478 0.00 0.00 0.00 3.53
364 555 4.080356 TCGACCATCTCATTTCCTTTCCAT 60.080 41.667 0.00 0.00 0.00 3.41
365 556 4.641989 CGACCATCTCATTTCCTTTCCATT 59.358 41.667 0.00 0.00 0.00 3.16
366 557 5.126061 CGACCATCTCATTTCCTTTCCATTT 59.874 40.000 0.00 0.00 0.00 2.32
367 558 6.535963 ACCATCTCATTTCCTTTCCATTTC 57.464 37.500 0.00 0.00 0.00 2.17
368 559 5.423290 ACCATCTCATTTCCTTTCCATTTCC 59.577 40.000 0.00 0.00 0.00 3.13
369 560 5.659971 CCATCTCATTTCCTTTCCATTTCCT 59.340 40.000 0.00 0.00 0.00 3.36
370 561 6.406624 CCATCTCATTTCCTTTCCATTTCCTG 60.407 42.308 0.00 0.00 0.00 3.86
372 563 3.515104 TCATTTCCTTTCCATTTCCTGGC 59.485 43.478 0.00 0.00 45.52 4.85
373 564 1.544724 TTCCTTTCCATTTCCTGGCG 58.455 50.000 0.00 0.00 45.52 5.69
374 565 0.404040 TCCTTTCCATTTCCTGGCGT 59.596 50.000 0.00 0.00 45.52 5.68
378 569 0.111446 TTCCATTTCCTGGCGTTCCA 59.889 50.000 0.00 0.00 45.52 3.53
394 585 7.107542 TGGCGTTCCAGATTAAAATAGTAACT 58.892 34.615 0.00 0.00 37.47 2.24
416 607 8.510243 AACTATGTGTCATTCAAATGCATAGA 57.490 30.769 22.22 0.00 38.20 1.98
424 615 7.147966 TGTCATTCAAATGCATAGAAAGCTCAT 60.148 33.333 15.77 0.00 36.36 2.90
458 649 1.169661 ACTTCGGTTTGAATGGCGCA 61.170 50.000 10.83 0.00 35.63 6.09
514 705 0.323725 GGTGAGCCCATGGTGATGTT 60.324 55.000 11.73 0.00 0.00 2.71
516 707 1.203052 GTGAGCCCATGGTGATGTTTG 59.797 52.381 11.73 0.00 0.00 2.93
536 727 3.032609 GGATGCTCCGCGTCATCG 61.033 66.667 19.69 0.87 45.37 3.84
585 811 7.824289 CCTAATTTGTACTCACTCCATCTTTGA 59.176 37.037 0.00 0.00 0.00 2.69
619 845 9.797556 ACTTATAACTTTTGGTTGAAGTCAAAC 57.202 29.630 1.98 1.98 43.57 2.93
621 847 4.776795 ACTTTTGGTTGAAGTCAAACGT 57.223 36.364 4.70 0.00 46.11 3.99
833 1081 5.010314 TGCCTAACATACCTACCATCGTAAG 59.990 44.000 0.00 0.00 0.00 2.34
903 1152 4.099573 TGAGACAAGAATCGTATTCTCCCC 59.900 45.833 9.54 4.12 30.44 4.81
1021 1271 2.785713 ATAAAGGTTGCGTTGCGTTT 57.214 40.000 0.00 0.00 0.00 3.60
1036 1286 2.356553 TTTCCTCCGACGTTGGCG 60.357 61.111 17.75 11.22 44.93 5.69
1087 1338 4.324267 CATGCAGCATCTCAATCTCCATA 58.676 43.478 4.38 0.00 0.00 2.74
1515 1766 0.107508 CCTCGTCCTCACCGGTAGTA 60.108 60.000 6.87 0.00 0.00 1.82
1517 1768 1.399791 CTCGTCCTCACCGGTAGTAAC 59.600 57.143 6.87 2.77 0.00 2.50
1524 1775 3.956199 CCTCACCGGTAGTAACTAATCCA 59.044 47.826 6.87 0.00 0.00 3.41
1531 1782 6.610425 ACCGGTAGTAACTAATCCAAGAATCT 59.390 38.462 4.49 0.00 0.00 2.40
1532 1783 7.781693 ACCGGTAGTAACTAATCCAAGAATCTA 59.218 37.037 4.49 0.00 0.00 1.98
1533 1784 8.081025 CCGGTAGTAACTAATCCAAGAATCTAC 58.919 40.741 0.00 0.00 0.00 2.59
1534 1785 8.848182 CGGTAGTAACTAATCCAAGAATCTACT 58.152 37.037 0.00 0.00 0.00 2.57
1535 1786 9.968870 GGTAGTAACTAATCCAAGAATCTACTG 57.031 37.037 0.00 0.00 0.00 2.74
1551 1802 9.877178 AGAATCTACTGTATTCACGAAAGAAAT 57.123 29.630 6.18 0.00 36.09 2.17
1557 1808 8.697846 ACTGTATTCACGAAAGAAATTATCGA 57.302 30.769 1.03 0.00 39.73 3.59
1567 1818 3.372954 AGAAATTATCGACCGAGAAGCG 58.627 45.455 5.72 0.00 40.47 4.68
1571 1822 1.589803 TATCGACCGAGAAGCGATCA 58.410 50.000 0.00 0.00 42.98 2.92
1581 1832 4.355437 CGAGAAGCGATCAAGAAGTGTAT 58.645 43.478 0.00 0.00 44.57 2.29
1615 1877 5.294060 TGATGTATGATCGATGTGTTTGTGG 59.706 40.000 0.54 0.00 0.00 4.17
1640 1902 1.244697 GCAGAGGAGAGTGACGACCA 61.245 60.000 0.00 0.00 0.00 4.02
1655 1917 1.954362 GACCAGAGCAGAGTGCCGAT 61.954 60.000 0.00 0.00 46.52 4.18
1818 2080 2.492090 CCGCTGGACTTCGAGGAG 59.508 66.667 0.00 0.00 0.00 3.69
2180 2449 0.531200 ACCAGAAGTCGACGGAATCC 59.469 55.000 10.46 0.00 0.00 3.01
2183 2452 1.202582 CAGAAGTCGACGGAATCCAGT 59.797 52.381 10.46 0.00 0.00 4.00
2192 2461 1.077429 GGAATCCAGTGTCCAGGGC 60.077 63.158 0.00 0.00 33.79 5.19
2380 2649 1.938577 CAAGATGATCACTTCCAGCGG 59.061 52.381 0.00 0.00 0.00 5.52
2408 2677 2.588989 CCCCAGCTCTGCTCTTCC 59.411 66.667 0.00 0.00 36.40 3.46
2501 2774 4.013728 TGTAATTCGCTTGCCTTACCAAT 58.986 39.130 0.00 0.00 0.00 3.16
2502 2775 3.508744 AATTCGCTTGCCTTACCAATG 57.491 42.857 0.00 0.00 0.00 2.82
2520 2793 0.460811 TGATGATGCTGTCGTCCTGC 60.461 55.000 8.70 1.12 41.35 4.85
2537 2815 2.743928 CCCTGCGCTGGACTTGTC 60.744 66.667 32.43 0.00 0.00 3.18
2568 2846 2.774687 ACGGGACATTTCAGTTGTACC 58.225 47.619 0.00 0.00 43.57 3.34
2587 2865 6.811954 TGTACCGCAGTAGAATCAATATCAA 58.188 36.000 0.00 0.00 0.00 2.57
2590 2868 5.702670 ACCGCAGTAGAATCAATATCAATGG 59.297 40.000 0.00 0.00 0.00 3.16
2609 2887 5.638596 ATGGTTAAAATCACGGGAGAAAC 57.361 39.130 0.00 0.00 0.00 2.78
2610 2888 4.462133 TGGTTAAAATCACGGGAGAAACA 58.538 39.130 0.00 0.00 0.00 2.83
2615 2893 8.083462 GGTTAAAATCACGGGAGAAACAAAATA 58.917 33.333 0.00 0.00 0.00 1.40
2652 2930 5.323371 TGCAGCGAAATTTTAGCCTAAAT 57.677 34.783 10.15 0.00 0.00 1.40
2653 2931 5.719173 TGCAGCGAAATTTTAGCCTAAATT 58.281 33.333 10.15 1.62 38.90 1.82
2676 2954 0.608640 ACAATATCCGGCGATCTCCC 59.391 55.000 9.30 0.00 0.00 4.30
2689 2967 0.251916 ATCTCCCGCGATTTTCACCA 59.748 50.000 8.23 0.00 0.00 4.17
2692 2970 2.485122 CCGCGATTTTCACCAGCC 59.515 61.111 8.23 0.00 0.00 4.85
2701 2979 0.597568 TTTCACCAGCCTGCAAATCG 59.402 50.000 0.00 0.00 0.00 3.34
2702 2980 1.865788 TTCACCAGCCTGCAAATCGC 61.866 55.000 0.00 0.00 42.89 4.58
2736 3024 0.520412 CCAAACCACGCGCGATTTAG 60.520 55.000 39.36 20.96 0.00 1.85
2747 3035 3.121778 CGCGCGATTTAGAATCATGATCA 59.878 43.478 28.94 0.00 0.00 2.92
2750 3038 5.562998 GCGCGATTTAGAATCATGATCAAAG 59.437 40.000 12.10 0.00 0.00 2.77
2753 3041 7.111179 CGCGATTTAGAATCATGATCAAAGTTG 59.889 37.037 9.06 5.98 0.00 3.16
2754 3042 8.124823 GCGATTTAGAATCATGATCAAAGTTGA 58.875 33.333 9.06 0.00 42.14 3.18
2755 3043 9.430838 CGATTTAGAATCATGATCAAAGTTGAC 57.569 33.333 9.06 0.00 40.49 3.18
2756 3044 9.430838 GATTTAGAATCATGATCAAAGTTGACG 57.569 33.333 9.06 0.00 40.49 4.35
2757 3045 7.905604 TTAGAATCATGATCAAAGTTGACGT 57.094 32.000 9.06 0.00 40.49 4.34
2758 3046 6.414408 AGAATCATGATCAAAGTTGACGTC 57.586 37.500 9.06 9.11 40.49 4.34
2760 3048 4.001618 TCATGATCAAAGTTGACGTCCA 57.998 40.909 14.12 0.00 40.49 4.02
2763 3051 4.545823 TGATCAAAGTTGACGTCCAAAC 57.454 40.909 14.12 11.75 40.49 2.93
2765 3053 1.666700 TCAAAGTTGACGTCCAAACCG 59.333 47.619 14.12 3.97 36.36 4.44
2766 3054 1.666700 CAAAGTTGACGTCCAAACCGA 59.333 47.619 14.12 0.00 36.36 4.69
2772 3060 1.232119 GACGTCCAAACCGAAACCAT 58.768 50.000 3.51 0.00 0.00 3.55
2776 3064 2.477189 CGTCCAAACCGAAACCATATGC 60.477 50.000 0.00 0.00 0.00 3.14
2780 3068 3.428862 CCAAACCGAAACCATATGCTTCC 60.429 47.826 0.00 0.00 0.00 3.46
2783 3071 1.949525 CCGAAACCATATGCTTCCAGG 59.050 52.381 0.00 0.00 0.00 4.45
2808 3096 1.608590 ACATTTCAGTTGCTCAACCCG 59.391 47.619 8.95 1.99 42.06 5.28
2809 3097 1.608590 CATTTCAGTTGCTCAACCCGT 59.391 47.619 8.95 0.00 42.06 5.28
2815 3103 0.442699 GTTGCTCAACCCGTCGAATC 59.557 55.000 1.45 0.00 35.36 2.52
2861 3152 4.305989 TGCTGAAACCATTGAACAGTTC 57.694 40.909 6.32 6.32 0.00 3.01
2870 3161 3.003689 CCATTGAACAGTTCAGGTGTGAC 59.996 47.826 15.61 0.00 41.38 3.67
2918 3212 3.756727 GCTGCCTTTGCCTCCTGC 61.757 66.667 0.00 0.00 41.77 4.85
2939 3233 3.181465 GCAATGTGCCTAGCTACTTAGGA 60.181 47.826 4.34 0.00 42.39 2.94
3133 3445 7.756395 ATTGCATAATCATTCTAACCCTGAG 57.244 36.000 0.00 0.00 0.00 3.35
3147 3459 2.300437 ACCCTGAGCTTCTGTAACAGTC 59.700 50.000 0.00 0.00 32.61 3.51
3152 3464 4.621991 TGAGCTTCTGTAACAGTCACTTC 58.378 43.478 0.00 0.00 32.61 3.01
3157 3469 6.374333 AGCTTCTGTAACAGTCACTTCAAAAA 59.626 34.615 0.00 0.00 32.61 1.94
3293 3607 9.374711 TGAATAAACTTGAAATAAACCCTCCTT 57.625 29.630 0.00 0.00 0.00 3.36
3310 3624 2.030007 TCCTTGATTTTGAGGCTTTGCG 60.030 45.455 0.00 0.00 32.93 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.372128 GGCTTGCCAACTTCGCTTG 60.372 57.895 6.79 0.00 0.00 4.01
61 62 1.339438 TGGAGAAGCATTGCACCTCTC 60.339 52.381 21.48 20.42 33.41 3.20
72 73 1.077930 GCAGCCATCTGGAGAAGCA 60.078 57.895 0.00 0.00 40.65 3.91
89 280 3.497031 GAGTTGCCCTTACGCCGC 61.497 66.667 0.00 0.00 0.00 6.53
103 294 1.407656 TTTGTGAGGGTCTGCCGAGT 61.408 55.000 0.00 0.00 34.97 4.18
112 303 1.705873 ACTCTCGTCTTTGTGAGGGT 58.294 50.000 0.00 0.00 41.06 4.34
126 317 1.536284 CGGCGAAATCCACCTACTCTC 60.536 57.143 0.00 0.00 0.00 3.20
133 324 1.287425 CTTACTCGGCGAAATCCACC 58.713 55.000 12.13 0.00 0.00 4.61
151 342 0.250209 CTTGCGCATCCTCTATGGCT 60.250 55.000 12.75 0.00 35.99 4.75
157 348 3.720601 TGGCCTTGCGCATCCTCT 61.721 61.111 12.75 0.00 40.31 3.69
161 352 1.865788 TTTCTGTGGCCTTGCGCATC 61.866 55.000 12.75 3.25 40.31 3.91
163 354 2.124060 TTTTCTGTGGCCTTGCGCA 61.124 52.632 5.66 5.66 40.31 6.09
190 381 2.885113 CAGCGAGATGACCGGTCA 59.115 61.111 37.79 37.79 44.59 4.02
192 383 3.381983 TGCAGCGAGATGACCGGT 61.382 61.111 6.92 6.92 38.35 5.28
194 385 2.887568 GGTGCAGCGAGATGACCG 60.888 66.667 0.00 0.00 0.00 4.79
202 393 2.358615 ATTGCTTCGGTGCAGCGA 60.359 55.556 34.84 34.84 44.27 4.93
244 435 6.317140 TCATTTCTTCACACATGGCTCTTATC 59.683 38.462 0.00 0.00 0.00 1.75
259 450 3.333381 TGGACATCCCCTTCATTTCTTCA 59.667 43.478 0.00 0.00 34.29 3.02
262 453 2.922283 ACTGGACATCCCCTTCATTTCT 59.078 45.455 0.00 0.00 34.29 2.52
265 456 2.025887 GTCACTGGACATCCCCTTCATT 60.026 50.000 0.00 0.00 43.73 2.57
277 468 0.326264 AGGAGCATTGGTCACTGGAC 59.674 55.000 16.99 0.00 43.55 4.02
283 474 0.614697 TCGAGGAGGAGCATTGGTCA 60.615 55.000 16.99 0.00 0.00 4.02
289 480 2.430610 GGCACTCGAGGAGGAGCAT 61.431 63.158 18.41 0.00 36.84 3.79
337 528 2.567169 AGGAAATGAGATGGTCGACACA 59.433 45.455 18.91 13.25 0.00 3.72
369 560 7.107542 AGTTACTATTTTAATCTGGAACGCCA 58.892 34.615 0.00 0.00 43.47 5.69
370 561 7.549615 AGTTACTATTTTAATCTGGAACGCC 57.450 36.000 0.00 0.00 0.00 5.68
394 585 7.916977 GCTTTCTATGCATTTGAATGACACATA 59.083 33.333 21.23 5.48 38.70 2.29
416 607 2.641815 ACTTCACTCCTCCATGAGCTTT 59.358 45.455 0.00 0.00 35.72 3.51
441 632 0.109365 CATGCGCCATTCAAACCGAA 60.109 50.000 4.18 0.00 38.22 4.30
458 649 2.683362 CTCATGACTTGAGCACATGCAT 59.317 45.455 6.64 0.00 45.16 3.96
564 755 7.773224 TCTTTTCAAAGATGGAGTGAGTACAAA 59.227 33.333 0.00 0.00 39.95 2.83
608 834 4.167554 ACTTTGCAACGTTTGACTTCAA 57.832 36.364 2.17 0.00 0.00 2.69
718 945 9.447040 GTAAGAAAAATCTTCAACAACTACCAC 57.553 33.333 0.00 0.00 0.00 4.16
764 1001 8.537858 GTGTTATTTTCTACTCCCTCCTCTAAA 58.462 37.037 0.00 0.00 0.00 1.85
766 1003 7.186972 TGTGTTATTTTCTACTCCCTCCTCTA 58.813 38.462 0.00 0.00 0.00 2.43
824 1072 1.732259 GTCCAGTTGTGCTTACGATGG 59.268 52.381 0.00 0.00 0.00 3.51
833 1081 0.586802 GTCTTTCGGTCCAGTTGTGC 59.413 55.000 0.00 0.00 0.00 4.57
903 1152 1.142748 GTCATCTGAGGGTGGCTCG 59.857 63.158 0.00 0.00 0.00 5.03
1036 1286 2.979130 GCCTTGAGAGTGGCGATAC 58.021 57.895 0.00 0.00 39.71 2.24
1087 1338 1.299926 GCCGTCGCCGAACTATCAT 60.300 57.895 0.00 0.00 35.63 2.45
1464 1715 1.082104 GGAAGCCAAACTTGTCGCG 60.082 57.895 0.00 0.00 39.29 5.87
1517 1768 9.186323 CGTGAATACAGTAGATTCTTGGATTAG 57.814 37.037 0.00 0.00 34.88 1.73
1524 1775 9.706691 TTTCTTTCGTGAATACAGTAGATTCTT 57.293 29.630 0.00 0.00 34.88 2.52
1531 1782 9.791820 TCGATAATTTCTTTCGTGAATACAGTA 57.208 29.630 0.00 0.00 34.60 2.74
1532 1783 8.592998 GTCGATAATTTCTTTCGTGAATACAGT 58.407 33.333 0.00 0.00 34.60 3.55
1533 1784 8.056571 GGTCGATAATTTCTTTCGTGAATACAG 58.943 37.037 0.00 0.00 34.60 2.74
1534 1785 7.253850 CGGTCGATAATTTCTTTCGTGAATACA 60.254 37.037 0.00 0.00 34.60 2.29
1535 1786 7.043854 TCGGTCGATAATTTCTTTCGTGAATAC 60.044 37.037 0.00 0.00 34.60 1.89
1536 1787 6.974048 TCGGTCGATAATTTCTTTCGTGAATA 59.026 34.615 0.00 0.00 34.60 1.75
1537 1788 5.808540 TCGGTCGATAATTTCTTTCGTGAAT 59.191 36.000 0.00 0.00 34.60 2.57
1551 1802 2.682952 GATCGCTTCTCGGTCGATAA 57.317 50.000 0.00 0.00 42.20 1.75
1557 1808 1.546476 ACTTCTTGATCGCTTCTCGGT 59.454 47.619 0.00 0.00 39.05 4.69
1567 1818 8.358895 TCAGATGATCAGATACACTTCTTGATC 58.641 37.037 0.09 5.97 34.44 2.92
1571 1822 8.020777 ACATCAGATGATCAGATACACTTCTT 57.979 34.615 17.81 0.00 31.21 2.52
1615 1877 0.681733 TCACTCTCCTCTGCCACAAC 59.318 55.000 0.00 0.00 0.00 3.32
1640 1902 1.674764 CCTCATCGGCACTCTGCTCT 61.675 60.000 0.00 0.00 44.28 4.09
1655 1917 0.907486 CATGAGCAGGTTCTCCCTCA 59.093 55.000 0.00 0.00 43.86 3.86
1818 2080 0.462759 CGTCCAGGATCTTGCCCTTC 60.463 60.000 0.00 0.00 0.00 3.46
2111 2377 2.200337 GCCTCCGTTGGTGCCTTTT 61.200 57.895 0.00 0.00 0.00 2.27
2180 2449 1.298014 GGAGAAGCCCTGGACACTG 59.702 63.158 0.00 0.00 0.00 3.66
2183 2452 0.032515 TATCGGAGAAGCCCTGGACA 60.033 55.000 0.00 0.00 43.58 4.02
2192 2461 0.952280 TAGCAGCGGTATCGGAGAAG 59.048 55.000 0.00 0.00 43.58 2.85
2501 2774 0.460811 GCAGGACGACAGCATCATCA 60.461 55.000 0.00 0.00 0.00 3.07
2502 2775 1.156645 GGCAGGACGACAGCATCATC 61.157 60.000 0.00 0.00 0.00 2.92
2520 2793 2.743928 GACAAGTCCAGCGCAGGG 60.744 66.667 19.70 15.42 0.00 4.45
2537 2815 1.238439 ATGTCCCGTTCAGTTTGCTG 58.762 50.000 0.00 0.00 43.87 4.41
2568 2846 6.791887 ACCATTGATATTGATTCTACTGCG 57.208 37.500 0.00 0.00 0.00 5.18
2587 2865 5.074115 TGTTTCTCCCGTGATTTTAACCAT 58.926 37.500 0.00 0.00 0.00 3.55
2590 2868 7.940178 ATTTTGTTTCTCCCGTGATTTTAAC 57.060 32.000 0.00 0.00 0.00 2.01
2652 2930 0.179032 ATCGCCGGATATTGTGCCAA 60.179 50.000 5.05 0.00 0.00 4.52
2653 2931 0.602638 GATCGCCGGATATTGTGCCA 60.603 55.000 5.05 0.00 31.51 4.92
2657 2935 0.608640 GGGAGATCGCCGGATATTGT 59.391 55.000 5.05 0.00 31.51 2.71
2658 2936 0.458543 CGGGAGATCGCCGGATATTG 60.459 60.000 16.62 0.00 31.51 1.90
2659 2937 1.890894 CGGGAGATCGCCGGATATT 59.109 57.895 16.62 0.00 31.51 1.28
2660 2938 3.604629 CGGGAGATCGCCGGATAT 58.395 61.111 16.62 0.00 31.51 1.63
2668 2946 0.577269 GTGAAAATCGCGGGAGATCG 59.423 55.000 6.13 0.00 0.00 3.69
2676 2954 1.135315 CAGGCTGGTGAAAATCGCG 59.865 57.895 6.61 0.00 0.00 5.87
2702 2980 4.776322 TGGCCATCGTTCGCCCTG 62.776 66.667 0.00 0.00 45.07 4.45
2703 2981 3.561120 TTTGGCCATCGTTCGCCCT 62.561 57.895 6.09 0.00 45.07 5.19
2705 2983 2.178273 GTTTGGCCATCGTTCGCC 59.822 61.111 6.09 0.00 45.92 5.54
2718 3006 0.440758 TCTAAATCGCGCGTGGTTTG 59.559 50.000 34.35 24.59 0.00 2.93
2722 3010 0.927537 TGATTCTAAATCGCGCGTGG 59.072 50.000 30.98 13.12 0.00 4.94
2724 3012 2.469826 TCATGATTCTAAATCGCGCGT 58.530 42.857 30.98 13.76 0.00 6.01
2726 3014 4.652175 TGATCATGATTCTAAATCGCGC 57.348 40.909 10.14 0.00 0.00 6.86
2728 3016 8.124823 TCAACTTTGATCATGATTCTAAATCGC 58.875 33.333 10.14 0.00 31.01 4.58
2736 3024 5.122239 TGGACGTCAACTTTGATCATGATTC 59.878 40.000 18.91 4.08 39.73 2.52
2747 3035 2.027003 TCGGTTTGGACGTCAACTTT 57.973 45.000 18.91 0.00 34.67 2.66
2750 3038 1.268184 GGTTTCGGTTTGGACGTCAAC 60.268 52.381 18.91 13.67 34.67 3.18
2753 3041 1.232119 ATGGTTTCGGTTTGGACGTC 58.768 50.000 7.13 7.13 0.00 4.34
2754 3042 2.547299 TATGGTTTCGGTTTGGACGT 57.453 45.000 0.00 0.00 0.00 4.34
2755 3043 2.477189 GCATATGGTTTCGGTTTGGACG 60.477 50.000 4.56 0.00 0.00 4.79
2756 3044 2.752903 AGCATATGGTTTCGGTTTGGAC 59.247 45.455 0.40 0.00 0.00 4.02
2757 3045 3.080300 AGCATATGGTTTCGGTTTGGA 57.920 42.857 0.40 0.00 0.00 3.53
2758 3046 3.428862 GGAAGCATATGGTTTCGGTTTGG 60.429 47.826 20.42 0.00 37.58 3.28
2760 3048 3.426615 TGGAAGCATATGGTTTCGGTTT 58.573 40.909 20.42 0.00 37.58 3.27
2763 3051 1.949525 CCTGGAAGCATATGGTTTCGG 59.050 52.381 22.87 22.87 37.58 4.30
2765 3053 4.016444 TGTTCCTGGAAGCATATGGTTTC 58.984 43.478 20.42 18.91 35.69 2.78
2766 3054 4.046286 TGTTCCTGGAAGCATATGGTTT 57.954 40.909 20.42 5.56 35.69 3.27
2772 3060 5.076182 TGAAATGTTGTTCCTGGAAGCATA 58.924 37.500 9.92 0.00 0.00 3.14
2776 3064 5.284079 CAACTGAAATGTTGTTCCTGGAAG 58.716 41.667 9.92 0.00 41.50 3.46
2780 3068 4.293415 GAGCAACTGAAATGTTGTTCCTG 58.707 43.478 11.35 0.00 45.76 3.86
2808 3096 5.356882 TTTCTGGAAACATGTGATTCGAC 57.643 39.130 0.00 0.00 41.51 4.20
2847 3138 2.951642 CACACCTGAACTGTTCAATGGT 59.048 45.455 25.90 24.11 38.37 3.55
2848 3139 3.003689 GTCACACCTGAACTGTTCAATGG 59.996 47.826 25.90 23.63 39.58 3.16
2852 3143 3.627395 AAGTCACACCTGAACTGTTCA 57.373 42.857 20.95 20.95 38.17 3.18
2861 3152 2.549754 GTCCACATGAAAGTCACACCTG 59.450 50.000 0.00 0.00 0.00 4.00
2870 3161 2.271800 GCCGAGTAGTCCACATGAAAG 58.728 52.381 0.00 0.00 0.00 2.62
2918 3212 4.672587 TCCTAAGTAGCTAGGCACATTG 57.327 45.455 0.00 0.00 38.73 2.82
2939 3233 3.118112 CCCTTGTCAGCCTCACAGATAAT 60.118 47.826 0.00 0.00 0.00 1.28
3002 3296 5.261209 AGTCATTTCTGATCTCCGAGAAG 57.739 43.478 1.27 0.00 32.98 2.85
3133 3445 5.734855 TTTGAAGTGACTGTTACAGAAGC 57.265 39.130 20.07 8.32 35.18 3.86
3157 3469 2.223845 GGCATTTTCTTTGCGTGCAATT 59.776 40.909 8.26 0.00 41.07 2.32
3158 3470 1.799994 GGCATTTTCTTTGCGTGCAAT 59.200 42.857 8.26 0.00 41.07 3.56
3164 3476 0.161446 GTTGCGGCATTTTCTTTGCG 59.839 50.000 2.28 0.00 41.07 4.85
3293 3607 1.602668 GCACGCAAAGCCTCAAAATCA 60.603 47.619 0.00 0.00 0.00 2.57
3310 3624 3.064207 TGTCGAAGTAGGTTTGATGCAC 58.936 45.455 0.00 0.00 30.78 4.57
3482 3798 3.969976 AGCTGGTAAAGGAGATATGCTCA 59.030 43.478 0.00 0.00 45.81 4.26


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

AutoCloner maintained by Alex Coulton.