Multiple sequence alignment - TraesCS3A01G319200

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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 TraesCS3A01G319200 chr3A 100.000 3206 0 0 1 3206 561122249 561119044 0.000000e+00 5921.0
1 TraesCS3A01G319200 chr3A 86.207 203 26 2 404 606 627696283 627696083 5.380000e-53 219.0
2 TraesCS3A01G319200 chr3D 89.276 3012 133 70 324 3206 426843140 426846090 0.000000e+00 3598.0
3 TraesCS3A01G319200 chr3D 93.210 324 19 2 1 324 426842782 426843102 1.040000e-129 473.0
4 TraesCS3A01G319200 chr3D 91.525 59 5 0 548 606 813675 813617 7.370000e-12 82.4
5 TraesCS3A01G319200 chr3D 87.931 58 7 0 329 386 813853 813796 5.740000e-08 69.4
6 TraesCS3A01G319200 chr3B 94.320 669 32 4 2540 3206 556487724 556488388 0.000000e+00 1020.0
7 TraesCS3A01G319200 chr3B 89.805 667 51 6 1713 2362 556487016 556487682 0.000000e+00 839.0
8 TraesCS3A01G319200 chr3B 87.647 680 36 13 937 1570 556486255 556486932 0.000000e+00 747.0
9 TraesCS3A01G319200 chr3B 92.105 114 8 1 212 324 43196381 43196494 3.310000e-35 159.0
10 TraesCS3A01G319200 chr3B 84.906 106 11 5 87 189 405779259 405779156 5.660000e-18 102.0
11 TraesCS3A01G319200 chr3B 74.820 278 37 8 329 606 43196540 43196784 9.470000e-16 95.3
12 TraesCS3A01G319200 chr3B 87.500 72 6 2 1 72 42166979 42167047 2.650000e-11 80.5
13 TraesCS3A01G319200 chr4A 86.124 209 22 2 608 809 601021782 601021574 5.380000e-53 219.0
14 TraesCS3A01G319200 chr4A 92.035 113 8 1 213 324 170812952 170812840 1.190000e-34 158.0
15 TraesCS3A01G319200 chr4A 92.727 55 4 0 548 602 170812617 170812563 2.650000e-11 80.5
16 TraesCS3A01G319200 chr4A 90.741 54 5 0 324 377 601022113 601022060 4.440000e-09 73.1
17 TraesCS3A01G319200 chr4A 88.333 60 6 1 329 388 170812794 170812736 1.600000e-08 71.3
18 TraesCS3A01G319200 chr4A 90.566 53 3 2 7 58 104105453 104105402 5.740000e-08 69.4
19 TraesCS3A01G319200 chr4A 90.566 53 3 2 7 58 702722424 702722373 5.740000e-08 69.4
20 TraesCS3A01G319200 chr4A 90.566 53 3 2 7 58 702722904 702722853 5.740000e-08 69.4
21 TraesCS3A01G319200 chr7A 78.899 327 48 17 1 324 83365162 83365470 5.420000e-48 202.0
22 TraesCS3A01G319200 chr7A 91.525 59 5 0 548 606 83365748 83365806 7.370000e-12 82.4
23 TraesCS3A01G319200 chr6A 78.899 327 48 17 1 324 187971179 187970871 5.420000e-48 202.0
24 TraesCS3A01G319200 chr6A 93.220 118 7 1 208 324 415100310 415100427 4.250000e-39 172.0
25 TraesCS3A01G319200 chr6A 91.525 59 5 0 548 606 187970003 187969945 7.370000e-12 82.4
26 TraesCS3A01G319200 chr6A 91.525 59 5 0 548 606 415101025 415101083 7.370000e-12 82.4
27 TraesCS3A01G319200 chr6D 78.816 321 46 20 10 324 446120417 446120113 2.520000e-46 196.0
28 TraesCS3A01G319200 chr6D 91.525 59 5 0 548 606 446119890 446119832 7.370000e-12 82.4
29 TraesCS3A01G319200 chr4D 78.176 307 46 17 24 324 386532699 386532408 3.290000e-40 176.0
30 TraesCS3A01G319200 chrUn 80.172 232 37 5 608 832 24454672 24454443 7.120000e-37 165.0
31 TraesCS3A01G319200 chr6B 89.516 124 10 2 202 324 420831780 420831901 1.540000e-33 154.0
32 TraesCS3A01G319200 chr6B 74.460 278 38 10 329 606 420831947 420832191 4.410000e-14 89.8
33 TraesCS3A01G319200 chr5D 76.636 214 36 10 499 704 66299506 66299713 4.370000e-19 106.0
34 TraesCS3A01G319200 chr5B 76.733 202 23 11 329 529 263784486 263784308 1.220000e-14 91.6
35 TraesCS3A01G319200 chr5B 88.136 59 5 2 1 58 377625992 377626049 5.740000e-08 69.4
36 TraesCS3A01G319200 chr4B 88.136 59 5 2 1 58 290361271 290361328 5.740000e-08 69.4
37 TraesCS3A01G319200 chr1B 88.136 59 5 2 1 58 489574481 489574538 5.740000e-08 69.4
38 TraesCS3A01G319200 chr1B 88.136 59 5 2 1 58 489575118 489575175 5.740000e-08 69.4


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 TraesCS3A01G319200 chr3A 561119044 561122249 3205 True 5921.000000 5921 100.000000 1 3206 1 chr3A.!!$R1 3205
1 TraesCS3A01G319200 chr3D 426842782 426846090 3308 False 2035.500000 3598 91.243000 1 3206 2 chr3D.!!$F1 3205
2 TraesCS3A01G319200 chr3B 556486255 556488388 2133 False 868.666667 1020 90.590667 937 3206 3 chr3B.!!$F3 2269

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
389 428 0.506932 AATAATGTCCGATTCGCGCG 59.493 50.0 26.76 26.76 39.11 6.86 F
1551 1690 0.101219 GCGTGAATTTCCCTGATGCC 59.899 55.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2278 0.743097 GGATGGCCAAAGCATCACTC 59.257 55.0 10.96 0.0 42.56 3.51 R
2723 2890 0.401356 TGAGGCAAGCCATTCAGTGA 59.599 50.0 14.40 0.0 38.92 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
205 206 0.811281 ATTTGGTGCCTAGCTTTCGC 59.189 50.000 0.00 0.00 0.00 4.70
250 251 8.678593 ACTACTAGCTAGCTTTTGTTCTTTTT 57.321 30.769 24.88 0.00 0.00 1.94
327 366 6.256912 TGTCTACATGTCGTTGTGTATGTA 57.743 37.500 0.00 0.00 35.55 2.29
363 402 3.449377 TCGGCTACAAATGACATGGACTA 59.551 43.478 0.00 0.00 0.00 2.59
364 403 4.081365 TCGGCTACAAATGACATGGACTAA 60.081 41.667 0.00 0.00 0.00 2.24
371 410 7.595819 ACAAATGACATGGACTAAAAAGGAA 57.404 32.000 0.00 0.00 0.00 3.36
372 411 8.193953 ACAAATGACATGGACTAAAAAGGAAT 57.806 30.769 0.00 0.00 0.00 3.01
379 418 8.293699 ACATGGACTAAAAAGGAATAATGTCC 57.706 34.615 0.00 0.00 41.97 4.02
385 424 7.916552 ACTAAAAAGGAATAATGTCCGATTCG 58.083 34.615 0.00 0.00 43.03 3.34
386 425 4.813296 AAAGGAATAATGTCCGATTCGC 57.187 40.909 0.00 0.00 43.03 4.70
387 426 2.404215 AGGAATAATGTCCGATTCGCG 58.596 47.619 0.00 0.00 43.03 5.87
388 427 1.136336 GGAATAATGTCCGATTCGCGC 60.136 52.381 0.00 0.00 39.11 6.86
389 428 0.506932 AATAATGTCCGATTCGCGCG 59.493 50.000 26.76 26.76 39.11 6.86
390 429 1.886861 ATAATGTCCGATTCGCGCGC 61.887 55.000 27.95 23.91 39.11 6.86
424 463 4.858680 GCGCAAGGGAGGTAGGGC 62.859 72.222 0.30 0.00 38.28 5.19
438 477 1.422977 TAGGGCCTGGAGTTTGCACA 61.423 55.000 18.53 0.00 0.00 4.57
444 483 1.447317 CTGGAGTTTGCACAAGCCGT 61.447 55.000 0.00 0.00 41.13 5.68
469 508 1.026718 CAGACGGTGATTGGAAGGGC 61.027 60.000 0.00 0.00 0.00 5.19
502 541 7.178097 TCTCGACCAGATATCAATCATGATCTT 59.822 37.037 9.06 0.00 42.75 2.40
518 557 5.843673 TGATCTTGCCTAACACAAACAAA 57.156 34.783 0.00 0.00 0.00 2.83
553 592 3.028850 CTCCCACCGTTACTCCAGATTA 58.971 50.000 0.00 0.00 0.00 1.75
554 593 3.443052 TCCCACCGTTACTCCAGATTAA 58.557 45.455 0.00 0.00 0.00 1.40
555 594 4.035112 TCCCACCGTTACTCCAGATTAAT 58.965 43.478 0.00 0.00 0.00 1.40
556 595 4.100498 TCCCACCGTTACTCCAGATTAATC 59.900 45.833 7.41 7.41 0.00 1.75
557 596 4.101119 CCCACCGTTACTCCAGATTAATCT 59.899 45.833 12.37 12.37 37.72 2.40
558 597 5.303589 CCCACCGTTACTCCAGATTAATCTA 59.696 44.000 17.53 2.80 34.85 1.98
559 598 6.214399 CCACCGTTACTCCAGATTAATCTAC 58.786 44.000 17.53 10.14 34.85 2.59
561 600 7.417570 CCACCGTTACTCCAGATTAATCTACTT 60.418 40.741 17.53 5.63 34.85 2.24
563 602 7.341256 ACCGTTACTCCAGATTAATCTACTTGA 59.659 37.037 17.53 10.72 34.85 3.02
565 604 9.186323 CGTTACTCCAGATTAATCTACTTGATG 57.814 37.037 17.53 4.82 34.85 3.07
648 714 2.305927 ACTCGGGACCAAATCTCATGTT 59.694 45.455 0.00 0.00 0.00 2.71
692 758 5.102953 TCCTACCCTCAGTTGATTCATTG 57.897 43.478 0.00 0.00 0.00 2.82
696 762 3.753272 ACCCTCAGTTGATTCATTGTTCG 59.247 43.478 0.00 0.00 0.00 3.95
728 794 2.869233 TTGTTTTGGAAGCTCACTGC 57.131 45.000 0.00 0.00 43.29 4.40
741 807 2.742372 ACTGCGCCGAATGACCAC 60.742 61.111 4.18 0.00 0.00 4.16
746 812 1.671054 CGCCGAATGACCACTGGTT 60.671 57.895 1.13 0.00 35.25 3.67
784 850 1.808945 GGCATGGACTTGTGAAGAGTG 59.191 52.381 0.00 0.00 0.00 3.51
785 851 1.808945 GCATGGACTTGTGAAGAGTGG 59.191 52.381 0.00 0.00 0.00 4.00
799 865 5.064452 GTGAAGAGTGGTGAGAATGCTTATG 59.936 44.000 0.00 0.00 0.00 1.90
845 925 2.213499 GATCTCCCGCACATTTACAGG 58.787 52.381 0.00 0.00 0.00 4.00
846 926 0.981183 TCTCCCGCACATTTACAGGT 59.019 50.000 0.00 0.00 0.00 4.00
847 927 2.181125 TCTCCCGCACATTTACAGGTA 58.819 47.619 0.00 0.00 0.00 3.08
972 1054 2.612471 CCAACTGAAGTCTGAGCTCTGG 60.612 54.545 19.23 8.62 0.00 3.86
1227 1349 2.579518 CGCACTCGCATAGACGCA 60.580 61.111 0.00 0.00 38.40 5.24
1452 1579 3.704566 TGTACATCTAGCAAGATCCGGTT 59.295 43.478 0.00 0.00 40.65 4.44
1491 1630 4.561735 TTACTTGTAGTGCCAAAACAGC 57.438 40.909 0.00 0.00 0.00 4.40
1504 1643 4.053295 CCAAAACAGCTGGATTTGTTGAG 58.947 43.478 29.64 18.62 37.57 3.02
1535 1674 2.009774 GCTAGTTGATGGTGAATGCGT 58.990 47.619 0.00 0.00 0.00 5.24
1543 1682 3.119531 TGATGGTGAATGCGTGAATTTCC 60.120 43.478 0.00 0.00 0.00 3.13
1551 1690 0.101219 GCGTGAATTTCCCTGATGCC 59.899 55.000 0.00 0.00 0.00 4.40
1555 1694 3.432186 CGTGAATTTCCCTGATGCCTCTA 60.432 47.826 0.00 0.00 0.00 2.43
1640 1784 5.106908 GGTTTTAGCTCAGTTCAGACATGTC 60.107 44.000 18.47 18.47 0.00 3.06
1717 1864 6.677781 TTACCCAAGCATTCTAGATTTTCG 57.322 37.500 0.00 0.00 0.00 3.46
1937 2100 6.707608 TCTTGCTCAATTCATATGAAGCGTAT 59.292 34.615 21.97 3.65 37.48 3.06
1940 2103 5.391310 GCTCAATTCATATGAAGCGTATGGG 60.391 44.000 21.97 15.50 37.48 4.00
1973 2136 6.701340 TCAGATGTATACTGTGTCTTGCTTT 58.299 36.000 4.17 0.00 36.81 3.51
1983 2146 6.729187 ACTGTGTCTTGCTTTCACTTTATTC 58.271 36.000 0.00 0.00 33.82 1.75
2061 2224 2.050077 GCAAGTGAGGCGCCAAAC 60.050 61.111 31.54 25.26 0.00 2.93
2114 2277 3.669557 GCGGATGCGAGTAACAATTTTGT 60.670 43.478 12.10 0.00 44.72 2.83
2115 2278 3.845775 CGGATGCGAGTAACAATTTTGTG 59.154 43.478 0.00 0.00 41.31 3.33
2211 2374 4.248691 TGATGATCTGTTCTGATAGGCG 57.751 45.455 0.00 0.00 0.00 5.52
2270 2433 6.601613 TGTTGTGCAATATTAGGGTCTTTAGG 59.398 38.462 0.00 0.00 0.00 2.69
2313 2480 4.824479 TCTCCTATCTTGTGATGTTGCA 57.176 40.909 0.00 0.00 34.32 4.08
2322 2489 1.072173 TGTGATGTTGCACTGTAGGCT 59.928 47.619 0.00 0.00 39.49 4.58
2387 2554 3.766676 AGCAGTGTCGTACTATGTGAG 57.233 47.619 0.00 0.00 37.60 3.51
2461 2628 9.701098 ATTACATTCGTACTAGAAACAAAGTGA 57.299 29.630 0.00 0.00 33.43 3.41
2466 2633 8.738199 TTCGTACTAGAAACAAAGTGATGTAG 57.262 34.615 0.00 0.00 32.02 2.74
2473 2640 6.872920 AGAAACAAAGTGATGTAGGCAAAAA 58.127 32.000 0.00 0.00 32.02 1.94
2501 2668 3.253432 CCAGAAAGCAACTCCTGGTTAAC 59.747 47.826 0.00 0.00 45.00 2.01
2503 2670 3.117663 AGAAAGCAACTCCTGGTTAACCA 60.118 43.478 25.58 25.58 45.00 3.67
2504 2671 3.306472 AAGCAACTCCTGGTTAACCAA 57.694 42.857 26.90 13.33 46.97 3.67
2505 2672 3.306472 AGCAACTCCTGGTTAACCAAA 57.694 42.857 26.90 17.06 46.97 3.28
2506 2673 3.637769 AGCAACTCCTGGTTAACCAAAA 58.362 40.909 26.90 16.73 46.97 2.44
2508 2675 4.653801 AGCAACTCCTGGTTAACCAAAATT 59.346 37.500 26.90 15.87 46.97 1.82
2509 2676 4.749598 GCAACTCCTGGTTAACCAAAATTG 59.250 41.667 26.90 24.84 46.97 2.32
2510 2677 5.683770 GCAACTCCTGGTTAACCAAAATTGT 60.684 40.000 26.90 17.48 46.97 2.71
2511 2678 5.529581 ACTCCTGGTTAACCAAAATTGTG 57.470 39.130 26.90 13.80 46.97 3.33
2513 2680 5.423931 ACTCCTGGTTAACCAAAATTGTGTT 59.576 36.000 26.90 3.48 46.97 3.32
2514 2681 5.908341 TCCTGGTTAACCAAAATTGTGTTC 58.092 37.500 26.90 0.00 46.97 3.18
2516 2683 5.983118 CCTGGTTAACCAAAATTGTGTTCTC 59.017 40.000 26.90 0.00 46.97 2.87
2517 2684 5.583495 TGGTTAACCAAAATTGTGTTCTCG 58.417 37.500 25.19 0.00 44.35 4.04
2518 2685 5.357314 TGGTTAACCAAAATTGTGTTCTCGA 59.643 36.000 25.19 0.00 44.35 4.04
2519 2686 5.684184 GGTTAACCAAAATTGTGTTCTCGAC 59.316 40.000 20.12 0.00 35.64 4.20
2520 2687 3.982576 ACCAAAATTGTGTTCTCGACC 57.017 42.857 0.00 0.00 0.00 4.79
2521 2688 3.283751 ACCAAAATTGTGTTCTCGACCA 58.716 40.909 0.00 0.00 0.00 4.02
2522 2689 3.315191 ACCAAAATTGTGTTCTCGACCAG 59.685 43.478 0.00 0.00 0.00 4.00
2523 2690 3.300009 CAAAATTGTGTTCTCGACCAGC 58.700 45.455 0.00 0.00 0.00 4.85
2524 2691 2.254546 AATTGTGTTCTCGACCAGCA 57.745 45.000 0.00 0.00 0.00 4.41
2525 2692 2.479566 ATTGTGTTCTCGACCAGCAT 57.520 45.000 0.00 0.00 0.00 3.79
2526 2693 3.610040 ATTGTGTTCTCGACCAGCATA 57.390 42.857 0.00 0.00 0.00 3.14
2527 2694 3.394674 TTGTGTTCTCGACCAGCATAA 57.605 42.857 0.00 0.00 0.00 1.90
2528 2695 3.394674 TGTGTTCTCGACCAGCATAAA 57.605 42.857 0.00 0.00 0.00 1.40
2529 2696 3.734463 TGTGTTCTCGACCAGCATAAAA 58.266 40.909 0.00 0.00 0.00 1.52
2530 2697 4.130857 TGTGTTCTCGACCAGCATAAAAA 58.869 39.130 0.00 0.00 0.00 1.94
2531 2698 4.213270 TGTGTTCTCGACCAGCATAAAAAG 59.787 41.667 0.00 0.00 0.00 2.27
2532 2699 4.213482 GTGTTCTCGACCAGCATAAAAAGT 59.787 41.667 0.00 0.00 0.00 2.66
2533 2700 5.407387 GTGTTCTCGACCAGCATAAAAAGTA 59.593 40.000 0.00 0.00 0.00 2.24
2534 2701 5.637810 TGTTCTCGACCAGCATAAAAAGTAG 59.362 40.000 0.00 0.00 0.00 2.57
2535 2702 4.181578 TCTCGACCAGCATAAAAAGTAGC 58.818 43.478 0.00 0.00 0.00 3.58
2536 2703 3.932710 CTCGACCAGCATAAAAAGTAGCA 59.067 43.478 0.00 0.00 0.00 3.49
2537 2704 4.320023 TCGACCAGCATAAAAAGTAGCAA 58.680 39.130 0.00 0.00 0.00 3.91
2538 2705 4.153475 TCGACCAGCATAAAAAGTAGCAAC 59.847 41.667 0.00 0.00 0.00 4.17
2581 2748 7.978414 CACATCATCTGTACTCCATGTATATCC 59.022 40.741 0.00 0.00 35.91 2.59
2606 2773 9.627123 CCTGGAAGAAATGGTATCAAATAGTTA 57.373 33.333 0.00 0.00 34.07 2.24
2661 2828 5.189180 AGTATCTGGGAAATGAGCAAGTTC 58.811 41.667 0.00 0.00 0.00 3.01
2723 2890 1.422531 TTGGACCTTGCCAGCATTTT 58.577 45.000 0.00 0.00 39.52 1.82
2932 3101 7.627088 GCATGTCTCACTAATGTTGCTACAAAT 60.627 37.037 4.79 0.19 37.91 2.32
3074 3262 5.381174 TGCATCATTTGTTGAAAGAGGAG 57.619 39.130 0.00 0.00 38.03 3.69
3077 3265 6.209986 TGCATCATTTGTTGAAAGAGGAGAAT 59.790 34.615 0.00 0.00 38.03 2.40
3115 3311 4.401022 TCTGCCTGCCCAATTATTCATAG 58.599 43.478 0.00 0.00 0.00 2.23
3116 3312 3.499338 TGCCTGCCCAATTATTCATAGG 58.501 45.455 0.00 0.00 0.00 2.57
3117 3313 3.139957 TGCCTGCCCAATTATTCATAGGA 59.860 43.478 0.00 0.00 0.00 2.94
3118 3314 4.202706 TGCCTGCCCAATTATTCATAGGAT 60.203 41.667 0.00 0.00 0.00 3.24
3119 3315 5.015072 TGCCTGCCCAATTATTCATAGGATA 59.985 40.000 0.00 0.00 0.00 2.59
3120 3316 5.591877 GCCTGCCCAATTATTCATAGGATAG 59.408 44.000 0.00 0.00 0.00 2.08
3121 3317 6.725364 CCTGCCCAATTATTCATAGGATAGT 58.275 40.000 0.00 0.00 0.00 2.12
3122 3318 6.600822 CCTGCCCAATTATTCATAGGATAGTG 59.399 42.308 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
222 223 8.678593 AAGAACAAAAGCTAGCTAGTAGTTTT 57.321 30.769 19.70 19.27 42.28 2.43
250 251 9.640963 CTAAGCTAGCTAGTAGTTTTTCTTTGA 57.359 33.333 19.70 0.47 34.31 2.69
300 301 8.626526 ACATACACAACGACATGTAGACATATA 58.373 33.333 13.30 0.55 34.88 0.86
316 317 6.086222 CCATCAACTGCTTTACATACACAAC 58.914 40.000 0.00 0.00 0.00 3.32
327 366 0.250901 AGCCGACCATCAACTGCTTT 60.251 50.000 0.00 0.00 0.00 3.51
363 402 5.578776 GCGAATCGGACATTATTCCTTTTT 58.421 37.500 4.35 0.00 32.88 1.94
364 403 4.260620 CGCGAATCGGACATTATTCCTTTT 60.261 41.667 0.00 0.00 32.88 2.27
371 410 1.886861 GCGCGCGAATCGGACATTAT 61.887 55.000 37.18 0.00 38.94 1.28
372 411 2.582265 GCGCGCGAATCGGACATTA 61.582 57.895 37.18 0.00 38.94 1.90
404 443 4.176752 CTACCTCCCTTGCGCCCC 62.177 72.222 4.18 0.00 0.00 5.80
408 447 4.176752 GGCCCTACCTCCCTTGCG 62.177 72.222 0.00 0.00 34.51 4.85
418 457 0.960861 GTGCAAACTCCAGGCCCTAC 60.961 60.000 0.00 0.00 0.00 3.18
424 463 1.662044 GGCTTGTGCAAACTCCAGG 59.338 57.895 0.00 0.00 41.91 4.45
428 467 4.614673 CACGGCTTGTGCAAACTC 57.385 55.556 0.00 0.00 42.70 3.01
438 477 4.578913 CGTCTGATGTCACGGCTT 57.421 55.556 0.00 0.00 32.19 4.35
444 483 1.899142 TCCAATCACCGTCTGATGTCA 59.101 47.619 0.00 0.00 38.82 3.58
445 484 2.672961 TCCAATCACCGTCTGATGTC 57.327 50.000 0.00 0.00 38.82 3.06
457 496 0.846427 ACCTCCTGCCCTTCCAATCA 60.846 55.000 0.00 0.00 0.00 2.57
502 541 4.727507 ACATGTTTGTTTGTGTTAGGCA 57.272 36.364 0.00 0.00 29.55 4.75
518 557 1.069049 GTGGGAGCAAGCAAAACATGT 59.931 47.619 0.00 0.00 0.00 3.21
605 644 8.922676 CGAGTCAACTTACTTCAGCTTATTAAA 58.077 33.333 0.00 0.00 0.00 1.52
619 685 2.825861 TTGGTCCCGAGTCAACTTAC 57.174 50.000 0.00 0.00 0.00 2.34
648 714 6.950041 AGGATTTCTCAGGATGTCAATTTGAA 59.050 34.615 0.00 0.00 37.40 2.69
681 747 5.914635 ACAACATGTCGAACAATGAATCAAC 59.085 36.000 0.00 0.00 0.00 3.18
692 758 6.402017 CAAAACAATGAACAACATGTCGAAC 58.598 36.000 0.00 0.00 39.39 3.95
696 762 6.509997 GCTTCCAAAACAATGAACAACATGTC 60.510 38.462 0.00 0.00 39.39 3.06
728 794 1.671054 AACCAGTGGTCATTCGGCG 60.671 57.895 17.06 0.00 33.12 6.46
741 807 5.278463 CCCTCTGTTTTAACATCACAACCAG 60.278 44.000 0.00 0.00 38.41 4.00
746 812 3.826524 TGCCCTCTGTTTTAACATCACA 58.173 40.909 0.00 0.00 38.41 3.58
759 825 0.325933 TCACAAGTCCATGCCCTCTG 59.674 55.000 0.00 0.00 0.00 3.35
784 850 9.364989 GTCTCTAATATCATAAGCATTCTCACC 57.635 37.037 0.00 0.00 0.00 4.02
785 851 9.071221 CGTCTCTAATATCATAAGCATTCTCAC 57.929 37.037 0.00 0.00 0.00 3.51
799 865 9.901724 CAAACAATAACACACGTCTCTAATATC 57.098 33.333 0.00 0.00 0.00 1.63
899 979 4.334203 TGCGGCGTTGTTTTTCTGATATAT 59.666 37.500 9.37 0.00 0.00 0.86
903 983 0.665835 TGCGGCGTTGTTTTTCTGAT 59.334 45.000 9.37 0.00 0.00 2.90
947 1029 3.471680 AGCTCAGACTTCAGTTGGTTTC 58.528 45.455 0.00 0.00 0.00 2.78
972 1054 0.535335 TCCGTACAGATTGAGGGTGC 59.465 55.000 0.00 0.00 0.00 5.01
1121 1212 2.278596 CCATCACTACGGACGGCG 60.279 66.667 4.80 4.80 0.00 6.46
1164 1285 2.386249 CGCGACTTTAGCTCTATCACC 58.614 52.381 0.00 0.00 0.00 4.02
1491 1630 3.383761 GTTTGCACCTCAACAAATCCAG 58.616 45.455 0.00 0.00 38.01 3.86
1504 1643 1.604604 TCAACTAGCTGGTTTGCACC 58.395 50.000 13.44 0.00 44.56 5.01
1519 1658 2.987413 TTCACGCATTCACCATCAAC 57.013 45.000 0.00 0.00 0.00 3.18
1535 1674 4.018506 TGTTAGAGGCATCAGGGAAATTCA 60.019 41.667 0.00 0.00 0.00 2.57
1551 1690 2.159028 GCCTGGTCTAGCCTTGTTAGAG 60.159 54.545 0.00 0.00 38.35 2.43
1555 1694 0.995024 ATGCCTGGTCTAGCCTTGTT 59.005 50.000 0.00 0.00 38.35 2.83
1737 1884 7.609146 TCAATCAACTTTGCAGAGATAATGAGT 59.391 33.333 11.85 6.30 0.00 3.41
1745 1893 7.445096 TCAAATAGTCAATCAACTTTGCAGAGA 59.555 33.333 11.85 0.00 0.00 3.10
1913 2076 5.165911 ACGCTTCATATGAATTGAGCAAG 57.834 39.130 18.26 8.98 33.01 4.01
1937 2100 0.850100 ACATCTGAAACCCACACCCA 59.150 50.000 0.00 0.00 0.00 4.51
1940 2103 5.351465 CACAGTATACATCTGAAACCCACAC 59.649 44.000 5.50 0.00 36.81 3.82
1973 2136 3.254657 CCAAAGGTTGGCGAATAAAGTGA 59.745 43.478 0.00 0.00 45.17 3.41
2061 2224 4.383774 TTGAACTACGCTTGTCGAATTG 57.616 40.909 0.00 0.00 41.67 2.32
2110 2273 1.340889 GGCCAAAGCATCACTCACAAA 59.659 47.619 0.00 0.00 42.56 2.83
2114 2277 1.466856 GATGGCCAAAGCATCACTCA 58.533 50.000 10.96 0.00 42.56 3.41
2115 2278 0.743097 GGATGGCCAAAGCATCACTC 59.257 55.000 10.96 0.00 42.56 3.51
2160 2323 1.234821 TTTCTCGCGCTTTGTGGATT 58.765 45.000 5.56 0.00 0.00 3.01
2211 2374 7.663043 TTTCTCCCTTATCTAGAGGAAGAAC 57.337 40.000 15.56 0.00 36.33 3.01
2270 2433 3.930634 ACCTCGGTTACAGTTAGACAC 57.069 47.619 0.00 0.00 0.00 3.67
2302 2469 1.072173 AGCCTACAGTGCAACATCACA 59.928 47.619 0.00 0.00 41.43 3.58
2443 2610 6.034683 GCCTACATCACTTTGTTTCTAGTACG 59.965 42.308 0.00 0.00 0.00 3.67
2473 2640 3.633986 CAGGAGTTGCTTTCTGGTTTCTT 59.366 43.478 0.00 0.00 0.00 2.52
2474 2641 3.217626 CAGGAGTTGCTTTCTGGTTTCT 58.782 45.455 0.00 0.00 0.00 2.52
2475 2642 2.294512 CCAGGAGTTGCTTTCTGGTTTC 59.705 50.000 0.00 0.00 41.21 2.78
2476 2643 2.310538 CCAGGAGTTGCTTTCTGGTTT 58.689 47.619 0.00 0.00 41.21 3.27
2477 2644 1.986882 CCAGGAGTTGCTTTCTGGTT 58.013 50.000 0.00 0.00 41.21 3.67
2478 2645 3.733709 CCAGGAGTTGCTTTCTGGT 57.266 52.632 0.00 0.00 41.21 4.00
2480 2647 3.253432 GGTTAACCAGGAGTTGCTTTCTG 59.747 47.826 20.12 0.00 39.67 3.02
2501 2668 3.853307 GCTGGTCGAGAACACAATTTTGG 60.853 47.826 0.00 0.00 0.00 3.28
2503 2670 2.948979 TGCTGGTCGAGAACACAATTTT 59.051 40.909 0.00 0.00 0.00 1.82
2504 2671 2.571212 TGCTGGTCGAGAACACAATTT 58.429 42.857 0.00 0.00 0.00 1.82
2505 2672 2.254546 TGCTGGTCGAGAACACAATT 57.745 45.000 0.00 0.00 0.00 2.32
2506 2673 2.479566 ATGCTGGTCGAGAACACAAT 57.520 45.000 0.00 0.00 0.00 2.71
2508 2675 3.394674 TTTATGCTGGTCGAGAACACA 57.605 42.857 0.00 0.00 0.00 3.72
2509 2676 4.213482 ACTTTTTATGCTGGTCGAGAACAC 59.787 41.667 0.00 0.00 0.00 3.32
2510 2677 4.385825 ACTTTTTATGCTGGTCGAGAACA 58.614 39.130 0.00 0.00 0.00 3.18
2511 2678 5.446073 GCTACTTTTTATGCTGGTCGAGAAC 60.446 44.000 0.00 0.00 0.00 3.01
2513 2680 4.181578 GCTACTTTTTATGCTGGTCGAGA 58.818 43.478 0.00 0.00 0.00 4.04
2514 2681 3.932710 TGCTACTTTTTATGCTGGTCGAG 59.067 43.478 0.00 0.00 0.00 4.04
2516 2683 4.083537 TGTTGCTACTTTTTATGCTGGTCG 60.084 41.667 0.00 0.00 0.00 4.79
2517 2684 5.371115 TGTTGCTACTTTTTATGCTGGTC 57.629 39.130 0.00 0.00 0.00 4.02
2518 2685 5.782893 TTGTTGCTACTTTTTATGCTGGT 57.217 34.783 0.00 0.00 0.00 4.00
2519 2686 8.755696 TTTATTGTTGCTACTTTTTATGCTGG 57.244 30.769 0.00 0.00 0.00 4.85
2529 2696 9.214957 GCCCTTTAAATTTTATTGTTGCTACTT 57.785 29.630 0.00 0.00 0.00 2.24
2530 2697 8.371699 TGCCCTTTAAATTTTATTGTTGCTACT 58.628 29.630 0.00 0.00 0.00 2.57
2531 2698 8.440059 GTGCCCTTTAAATTTTATTGTTGCTAC 58.560 33.333 0.00 0.00 0.00 3.58
2532 2699 8.150945 TGTGCCCTTTAAATTTTATTGTTGCTA 58.849 29.630 0.00 0.00 0.00 3.49
2533 2700 6.995091 TGTGCCCTTTAAATTTTATTGTTGCT 59.005 30.769 0.00 0.00 0.00 3.91
2534 2701 7.195839 TGTGCCCTTTAAATTTTATTGTTGC 57.804 32.000 0.00 0.00 0.00 4.17
2535 2702 8.997323 TGATGTGCCCTTTAAATTTTATTGTTG 58.003 29.630 0.00 0.00 0.00 3.33
2536 2703 9.737844 ATGATGTGCCCTTTAAATTTTATTGTT 57.262 25.926 0.00 0.00 0.00 2.83
2537 2704 9.382275 GATGATGTGCCCTTTAAATTTTATTGT 57.618 29.630 0.00 0.00 0.00 2.71
2538 2705 9.603921 AGATGATGTGCCCTTTAAATTTTATTG 57.396 29.630 0.00 0.00 0.00 1.90
2606 2773 9.490379 GTAAATAATAGCTTGTGTGTATAGGCT 57.510 33.333 0.00 0.00 0.00 4.58
2661 2828 0.671781 CTCGCCCACACTGAGAAAGG 60.672 60.000 0.00 0.00 31.31 3.11
2723 2890 0.401356 TGAGGCAAGCCATTCAGTGA 59.599 50.000 14.40 0.00 38.92 3.41
3074 3262 8.887717 CAGGCAGATATTATTACAAGGCTATTC 58.112 37.037 0.00 0.00 0.00 1.75
3077 3265 6.173339 GCAGGCAGATATTATTACAAGGCTA 58.827 40.000 0.00 0.00 0.00 3.93
3115 3311 6.582636 TCAACCAGTCATATCAACACTATCC 58.417 40.000 0.00 0.00 0.00 2.59
3116 3312 8.668510 AATCAACCAGTCATATCAACACTATC 57.331 34.615 0.00 0.00 0.00 2.08
3117 3313 9.547753 GTAATCAACCAGTCATATCAACACTAT 57.452 33.333 0.00 0.00 0.00 2.12
3118 3314 8.758829 AGTAATCAACCAGTCATATCAACACTA 58.241 33.333 0.00 0.00 0.00 2.74
3119 3315 7.550551 CAGTAATCAACCAGTCATATCAACACT 59.449 37.037 0.00 0.00 0.00 3.55
3120 3316 7.334421 ACAGTAATCAACCAGTCATATCAACAC 59.666 37.037 0.00 0.00 0.00 3.32
3121 3317 7.394016 ACAGTAATCAACCAGTCATATCAACA 58.606 34.615 0.00 0.00 0.00 3.33
3122 3318 7.549134 TGACAGTAATCAACCAGTCATATCAAC 59.451 37.037 0.00 0.00 38.19 3.18


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

AutoCloner maintained by Alex Coulton.