Multiple sequence alignment - TraesCS1B01G120100

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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 TraesCS1B01G120100 chr1B 100.000 2819 0 0 1 2819 142135488 142132670 0.000000e+00 5206.0
1 TraesCS1B01G120100 chr1B 89.892 1484 83 24 705 2146 142037212 142038670 0.000000e+00 1847.0
2 TraesCS1B01G120100 chr1B 87.803 1607 89 44 704 2257 141844699 141846251 0.000000e+00 1783.0
3 TraesCS1B01G120100 chr1B 90.414 1377 83 16 705 2048 142093472 142094832 0.000000e+00 1766.0
4 TraesCS1B01G120100 chr1B 86.916 107 13 1 2309 2415 141846345 141846450 4.930000e-23 119.0
5 TraesCS1B01G120100 chr1B 89.247 93 10 0 671 763 142036287 142036379 1.770000e-22 117.0
6 TraesCS1B01G120100 chr1B 93.750 48 3 0 2735 2782 142103366 142103413 3.900000e-09 73.1
7 TraesCS1B01G120100 chr1D 93.076 1733 68 25 700 2389 88282866 88281143 0.000000e+00 2488.0
8 TraesCS1B01G120100 chr1D 91.253 1429 65 24 758 2148 87903421 87904827 0.000000e+00 1892.0
9 TraesCS1B01G120100 chr1D 93.763 946 54 3 718 1661 88208045 88208987 0.000000e+00 1415.0
10 TraesCS1B01G120100 chr1D 91.817 721 30 10 1558 2257 88243854 88243142 0.000000e+00 977.0
11 TraesCS1B01G120100 chr1D 95.442 373 17 0 2426 2798 88242987 88242615 1.870000e-166 595.0
12 TraesCS1B01G120100 chr1D 86.914 512 25 17 1658 2148 88215120 88215610 1.150000e-148 536.0
13 TraesCS1B01G120100 chr1D 78.414 227 37 10 2200 2423 87905029 87905246 1.360000e-28 137.0
14 TraesCS1B01G120100 chr1D 93.617 47 3 0 2736 2782 88216304 88216350 1.400000e-08 71.3
15 TraesCS1B01G120100 chr1A 84.179 2326 182 66 167 2375 84797539 84795283 0.000000e+00 2085.0
16 TraesCS1B01G120100 chr1A 90.781 1486 64 17 787 2247 85006766 85005329 0.000000e+00 1917.0
17 TraesCS1B01G120100 chr1A 89.462 892 52 15 1278 2148 84484045 84484915 0.000000e+00 1088.0
18 TraesCS1B01G120100 chr1A 89.354 883 52 15 1287 2148 84621251 84622112 0.000000e+00 1072.0
19 TraesCS1B01G120100 chr1A 94.920 374 18 1 2426 2798 84795289 84794916 4.050000e-163 584.0
20 TraesCS1B01G120100 chr1A 83.758 314 39 9 312 619 84055585 84055892 1.280000e-73 287.0
21 TraesCS1B01G120100 chr1A 83.489 321 40 10 312 626 84620731 84621044 1.280000e-73 287.0
22 TraesCS1B01G120100 chr1A 93.750 48 2 1 2540 2587 84485526 84485572 1.400000e-08 71.3
23 TraesCS1B01G120100 chr1A 93.750 48 2 1 2540 2587 84622727 84622773 1.400000e-08 71.3
24 TraesCS1B01G120100 chr4D 90.721 1595 86 25 679 2257 464798255 464796707 0.000000e+00 2069.0
25 TraesCS1B01G120100 chr4D 86.029 680 49 22 2 642 464799001 464798329 0.000000e+00 688.0
26 TraesCS1B01G120100 chr4D 89.323 384 23 6 2426 2807 464796552 464796185 1.530000e-127 466.0
27 TraesCS1B01G120100 chr4D 96.875 64 1 1 2313 2376 464796607 464796545 3.840000e-19 106.0
28 TraesCS1B01G120100 chr3B 89.930 1142 73 16 1028 2148 535705558 535704438 0.000000e+00 1434.0
29 TraesCS1B01G120100 chr3B 77.632 228 31 11 2200 2423 535704246 535704035 1.370000e-23 121.0
30 TraesCS1B01G120100 chr5A 77.657 367 45 24 60 393 19221455 19221817 3.710000e-44 189.0
31 TraesCS1B01G120100 chr5B 94.737 38 2 0 66 103 491038178 491038215 3.030000e-05 60.2


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 TraesCS1B01G120100 chr1B 142132670 142135488 2818 True 5206.000000 5206 100.000000 1 2819 1 chr1B.!!$R1 2818
1 TraesCS1B01G120100 chr1B 142093472 142094832 1360 False 1766.000000 1766 90.414000 705 2048 1 chr1B.!!$F1 1343
2 TraesCS1B01G120100 chr1B 142036287 142038670 2383 False 982.000000 1847 89.569500 671 2146 2 chr1B.!!$F4 1475
3 TraesCS1B01G120100 chr1B 141844699 141846450 1751 False 951.000000 1783 87.359500 704 2415 2 chr1B.!!$F3 1711
4 TraesCS1B01G120100 chr1D 88281143 88282866 1723 True 2488.000000 2488 93.076000 700 2389 1 chr1D.!!$R1 1689
5 TraesCS1B01G120100 chr1D 88208045 88208987 942 False 1415.000000 1415 93.763000 718 1661 1 chr1D.!!$F1 943
6 TraesCS1B01G120100 chr1D 87903421 87905246 1825 False 1014.500000 1892 84.833500 758 2423 2 chr1D.!!$F2 1665
7 TraesCS1B01G120100 chr1D 88242615 88243854 1239 True 786.000000 977 93.629500 1558 2798 2 chr1D.!!$R2 1240
8 TraesCS1B01G120100 chr1D 88215120 88216350 1230 False 303.650000 536 90.265500 1658 2782 2 chr1D.!!$F3 1124
9 TraesCS1B01G120100 chr1A 85005329 85006766 1437 True 1917.000000 1917 90.781000 787 2247 1 chr1A.!!$R1 1460
10 TraesCS1B01G120100 chr1A 84794916 84797539 2623 True 1334.500000 2085 89.549500 167 2798 2 chr1A.!!$R2 2631
11 TraesCS1B01G120100 chr1A 84484045 84485572 1527 False 579.650000 1088 91.606000 1278 2587 2 chr1A.!!$F2 1309
12 TraesCS1B01G120100 chr1A 84620731 84622773 2042 False 476.766667 1072 88.864333 312 2587 3 chr1A.!!$F3 2275
13 TraesCS1B01G120100 chr4D 464796185 464799001 2816 True 832.250000 2069 90.737000 2 2807 4 chr4D.!!$R1 2805
14 TraesCS1B01G120100 chr3B 535704035 535705558 1523 True 777.500000 1434 83.781000 1028 2423 2 chr3B.!!$R1 1395

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
256 283 0.109781 AACATTCACGCGTGCATTCC 60.11 50.0 33.63 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2316 0.038251 CTAACTCAGTGTCAGCGGCA 60.038 55.0 1.45 0.0 0.0 5.69 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
19 20 1.986757 GAGGCAGAGACTGGGCAGA 60.987 63.158 0.00 0.00 31.21 4.26
28 29 3.196685 AGAGACTGGGCAGACAATAACTC 59.803 47.826 0.00 0.00 0.00 3.01
38 39 5.324697 GCAGACAATAACTCGGACAATTTC 58.675 41.667 0.00 0.00 0.00 2.17
41 42 7.148474 GCAGACAATAACTCGGACAATTTCTAA 60.148 37.037 0.00 0.00 0.00 2.10
64 66 0.319986 TAGTGGATGCGTGCGAAACA 60.320 50.000 0.00 0.00 0.00 2.83
72 74 0.908505 GCGTGCGAAACAAACGAAAA 59.091 45.000 0.00 0.00 39.64 2.29
80 82 5.006844 TGCGAAACAAACGAAAAGACTATGA 59.993 36.000 0.00 0.00 0.00 2.15
85 87 7.787725 AACAAACGAAAAGACTATGAACTCT 57.212 32.000 0.00 0.00 0.00 3.24
86 88 7.409465 ACAAACGAAAAGACTATGAACTCTC 57.591 36.000 0.00 0.00 0.00 3.20
123 126 9.522804 AGAGATATTCGAAAATGTTCTACAGAC 57.477 33.333 0.00 0.00 0.00 3.51
125 128 9.307121 AGATATTCGAAAATGTTCTACAGACTG 57.693 33.333 0.00 0.00 0.00 3.51
256 283 0.109781 AACATTCACGCGTGCATTCC 60.110 50.000 33.63 0.00 0.00 3.01
271 298 6.508404 GCGTGCATTCCAAAAATATTCATCAC 60.508 38.462 0.00 0.00 0.00 3.06
482 544 6.631016 AGAAAAGGGAAAAAGAAGTGTTCAC 58.369 36.000 0.00 0.00 0.00 3.18
483 545 5.993748 AAAGGGAAAAAGAAGTGTTCACA 57.006 34.783 5.74 0.00 0.00 3.58
484 546 6.544928 AAAGGGAAAAAGAAGTGTTCACAT 57.455 33.333 5.74 0.00 0.00 3.21
485 547 7.654022 AAAGGGAAAAAGAAGTGTTCACATA 57.346 32.000 5.74 0.00 0.00 2.29
489 551 9.362151 AGGGAAAAAGAAGTGTTCACATATTTA 57.638 29.630 5.74 0.00 0.00 1.40
490 552 9.406828 GGGAAAAAGAAGTGTTCACATATTTAC 57.593 33.333 5.74 2.66 0.00 2.01
496 558 9.744468 AAGAAGTGTTCACATATTTACAAAACC 57.256 29.630 5.74 0.00 0.00 3.27
498 560 9.394477 GAAGTGTTCACATATTTACAAAACCTC 57.606 33.333 5.74 0.00 0.00 3.85
499 561 7.581476 AGTGTTCACATATTTACAAAACCTCG 58.419 34.615 5.74 0.00 0.00 4.63
500 562 7.442969 AGTGTTCACATATTTACAAAACCTCGA 59.557 33.333 5.74 0.00 0.00 4.04
501 563 8.234546 GTGTTCACATATTTACAAAACCTCGAT 58.765 33.333 0.00 0.00 0.00 3.59
502 564 8.788806 TGTTCACATATTTACAAAACCTCGATT 58.211 29.630 0.00 0.00 0.00 3.34
505 567 8.240682 TCACATATTTACAAAACCTCGATTTGG 58.759 33.333 13.07 1.60 41.08 3.28
506 568 8.026607 CACATATTTACAAAACCTCGATTTGGT 58.973 33.333 13.07 5.97 41.08 3.67
507 569 8.026607 ACATATTTACAAAACCTCGATTTGGTG 58.973 33.333 13.07 0.00 41.08 4.17
508 570 4.839668 TTACAAAACCTCGATTTGGTGG 57.160 40.909 13.07 0.20 41.08 4.61
509 571 1.960689 ACAAAACCTCGATTTGGTGGG 59.039 47.619 13.07 0.00 41.08 4.61
510 572 2.235016 CAAAACCTCGATTTGGTGGGA 58.765 47.619 2.65 0.00 37.93 4.37
512 574 2.668144 AACCTCGATTTGGTGGGAAA 57.332 45.000 0.00 0.00 37.93 3.13
513 575 2.899303 ACCTCGATTTGGTGGGAAAT 57.101 45.000 0.00 0.00 36.30 2.17
515 577 3.617284 ACCTCGATTTGGTGGGAAATAC 58.383 45.455 0.00 0.00 36.30 1.89
516 578 2.612212 CCTCGATTTGGTGGGAAATACG 59.388 50.000 0.00 0.00 0.00 3.06
517 579 3.267483 CTCGATTTGGTGGGAAATACGT 58.733 45.455 0.00 0.00 0.00 3.57
518 580 3.004171 TCGATTTGGTGGGAAATACGTG 58.996 45.455 0.00 0.00 0.00 4.49
519 581 2.745281 CGATTTGGTGGGAAATACGTGT 59.255 45.455 0.00 0.00 0.00 4.49
520 582 3.189702 CGATTTGGTGGGAAATACGTGTT 59.810 43.478 0.00 0.00 0.00 3.32
521 583 4.670735 CGATTTGGTGGGAAATACGTGTTC 60.671 45.833 0.00 1.34 0.00 3.18
522 584 2.932855 TGGTGGGAAATACGTGTTCA 57.067 45.000 13.73 0.00 0.00 3.18
524 586 3.340034 TGGTGGGAAATACGTGTTCATC 58.660 45.455 13.73 2.85 0.00 2.92
525 587 3.008594 TGGTGGGAAATACGTGTTCATCT 59.991 43.478 13.73 0.00 0.00 2.90
527 589 5.104693 TGGTGGGAAATACGTGTTCATCTAT 60.105 40.000 13.73 0.00 0.00 1.98
529 591 7.159372 GGTGGGAAATACGTGTTCATCTATAT 58.841 38.462 13.73 0.00 0.00 0.86
530 592 7.660208 GGTGGGAAATACGTGTTCATCTATATT 59.340 37.037 13.73 0.00 0.00 1.28
531 593 9.701098 GTGGGAAATACGTGTTCATCTATATTA 57.299 33.333 13.73 0.00 0.00 0.98
643 705 9.696917 AACTTGTATTTTTGCAATAGAAGAAGG 57.303 29.630 17.57 2.30 37.12 3.46
644 706 9.077885 ACTTGTATTTTTGCAATAGAAGAAGGA 57.922 29.630 17.57 0.00 37.12 3.36
667 729 9.029368 AGGAATAAAAATGAGAAAAAGAGGAGG 57.971 33.333 0.00 0.00 0.00 4.30
668 730 7.761704 GGAATAAAAATGAGAAAAAGAGGAGGC 59.238 37.037 0.00 0.00 0.00 4.70
669 731 8.427902 AATAAAAATGAGAAAAAGAGGAGGCT 57.572 30.769 0.00 0.00 0.00 4.58
670 732 9.533831 AATAAAAATGAGAAAAAGAGGAGGCTA 57.466 29.630 0.00 0.00 0.00 3.93
671 733 7.839680 AAAAATGAGAAAAAGAGGAGGCTAA 57.160 32.000 0.00 0.00 0.00 3.09
674 736 9.533831 AAAATGAGAAAAAGAGGAGGCTAATTA 57.466 29.630 0.00 0.00 0.00 1.40
675 737 8.512966 AATGAGAAAAAGAGGAGGCTAATTAC 57.487 34.615 0.00 0.00 0.00 1.89
709 956 4.900635 CGGATGGATCGGAAAGAAAAAT 57.099 40.909 0.00 0.00 0.00 1.82
1113 1382 3.555168 CCGACTACAAGAAGCTTGAGGTT 60.555 47.826 2.10 0.00 38.61 3.50
1402 1671 0.468214 CTGGAGGCCTGTATCCGAGA 60.468 60.000 12.00 0.00 38.52 4.04
1524 1793 1.671054 CTTCTTCGGCGGGCTCAAA 60.671 57.895 7.21 0.00 0.00 2.69
1752 2037 2.329690 CTCGCCGAGACCAGATCG 59.670 66.667 8.82 0.00 39.86 3.69
1888 2173 2.203280 CCAGCACCGGTGGTTCAA 60.203 61.111 35.55 0.00 45.06 2.69
1904 2189 1.172180 TCAACAAGCCCAAAGGAGCG 61.172 55.000 0.00 0.00 33.47 5.03
1995 2316 7.322664 CCACTGGTTAATTATTTCATTGCAGT 58.677 34.615 0.00 0.00 0.00 4.40
1996 2317 7.276218 CCACTGGTTAATTATTTCATTGCAGTG 59.724 37.037 2.16 2.16 35.12 3.66
1997 2318 6.813152 ACTGGTTAATTATTTCATTGCAGTGC 59.187 34.615 8.58 8.58 0.00 4.40
1998 2319 6.105333 TGGTTAATTATTTCATTGCAGTGCC 58.895 36.000 13.72 0.00 0.00 5.01
1999 2320 5.231991 GGTTAATTATTTCATTGCAGTGCCG 59.768 40.000 13.72 0.88 0.00 5.69
2000 2321 2.276472 TTATTTCATTGCAGTGCCGC 57.724 45.000 13.72 0.00 0.00 6.53
2101 2435 1.964223 TCCTCGCCATGTAATCCTCTC 59.036 52.381 0.00 0.00 0.00 3.20
2148 2523 6.832900 TGTAGCATGGAAATTACATGATGGAA 59.167 34.615 21.50 3.25 46.60 3.53
2197 2746 3.758554 GTCTGAATCTGCTAAAGGCCAAA 59.241 43.478 5.01 0.00 40.92 3.28
2226 2779 6.656902 TGAATCTGGTTGAGCTTTCTATGAT 58.343 36.000 0.00 0.00 0.00 2.45
2231 2784 3.557595 GGTTGAGCTTTCTATGATCGGTG 59.442 47.826 0.00 0.00 0.00 4.94
2257 2810 4.815533 TCTGCTAAGCTTCTGAATCTGT 57.184 40.909 0.00 0.00 0.00 3.41
2259 2812 3.515630 TGCTAAGCTTCTGAATCTGTCG 58.484 45.455 0.00 0.00 0.00 4.35
2261 2814 2.393271 AAGCTTCTGAATCTGTCGGG 57.607 50.000 0.00 0.00 32.90 5.14
2262 2815 0.107945 AGCTTCTGAATCTGTCGGGC 60.108 55.000 0.00 0.00 32.90 6.13
2263 2816 0.107945 GCTTCTGAATCTGTCGGGCT 60.108 55.000 0.00 0.00 32.90 5.19
2286 2860 6.371548 GCTAAATACAGATGTGAAGTCCAACA 59.628 38.462 0.00 0.00 0.00 3.33
2288 2862 6.560253 AATACAGATGTGAAGTCCAACAAC 57.440 37.500 0.00 0.00 0.00 3.32
2305 2879 5.006552 CCAACAACGAAAAACAAATGCTGAT 59.993 36.000 0.00 0.00 0.00 2.90
2365 2962 2.034432 ACGCACATGAAATCTGCACAAA 59.966 40.909 0.00 0.00 0.00 2.83
2392 2990 8.352942 AGTAAACAGGCAATCAAGTTTTTCTAG 58.647 33.333 0.00 0.00 35.90 2.43
2395 2993 7.346751 ACAGGCAATCAAGTTTTTCTAGAAA 57.653 32.000 13.99 13.99 0.00 2.52
2407 3005 9.626045 AAGTTTTTCTAGAAACAACAAAGACTG 57.374 29.630 26.81 0.00 40.98 3.51
2429 3027 6.071952 ACTGAAATTCTTTGATGTGCGGTAAT 60.072 34.615 0.00 0.00 0.00 1.89
2470 3069 8.668510 AAAGATGGCACTAACAGATAATACAG 57.331 34.615 0.00 0.00 0.00 2.74
2474 3099 6.573434 TGGCACTAACAGATAATACAGTGAG 58.427 40.000 0.00 0.00 36.37 3.51
2502 3129 5.278315 GGGAACATCCGCATAAAAATCCTAC 60.278 44.000 0.00 0.00 37.43 3.18
2807 3443 1.066573 CCAGGTGACTCCACTCATCAC 60.067 57.143 0.00 0.00 42.77 3.06
2808 3444 1.898472 CAGGTGACTCCACTCATCACT 59.102 52.381 3.83 0.00 42.00 3.41
2809 3445 2.094286 CAGGTGACTCCACTCATCACTC 60.094 54.545 3.83 0.00 42.00 3.51
2810 3446 1.895798 GGTGACTCCACTCATCACTCA 59.104 52.381 3.83 0.00 42.00 3.41
2811 3447 2.499289 GGTGACTCCACTCATCACTCAT 59.501 50.000 3.83 0.00 42.00 2.90
2812 3448 3.430098 GGTGACTCCACTCATCACTCATC 60.430 52.174 3.83 0.00 42.00 2.92
2813 3449 3.194329 GTGACTCCACTCATCACTCATCA 59.806 47.826 0.00 0.00 39.72 3.07
2814 3450 3.446516 TGACTCCACTCATCACTCATCAG 59.553 47.826 0.00 0.00 0.00 2.90
2815 3451 3.439154 ACTCCACTCATCACTCATCAGT 58.561 45.455 0.00 0.00 0.00 3.41
2816 3452 8.983097 GTGACTCCACTCATCACTCATCAGTG 62.983 50.000 0.00 0.00 44.11 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.368190 CTGCCCAGTCTCTGCCTCG 62.368 68.421 0.00 0.00 0.00 4.63
11 12 1.207089 TCCGAGTTATTGTCTGCCCAG 59.793 52.381 0.00 0.00 0.00 4.45
28 29 7.432252 GCATCCACTAAATTTAGAAATTGTCCG 59.568 37.037 27.92 10.34 38.53 4.79
38 39 3.308595 TCGCACGCATCCACTAAATTTAG 59.691 43.478 21.21 21.21 36.82 1.85
41 42 1.732941 TCGCACGCATCCACTAAATT 58.267 45.000 0.00 0.00 0.00 1.82
64 66 6.760291 AGGAGAGTTCATAGTCTTTTCGTTT 58.240 36.000 0.00 0.00 34.15 3.60
188 191 5.592054 TGAAATACACGGCAAACATTTTCA 58.408 33.333 0.00 0.00 31.50 2.69
198 201 5.446143 ACATTTTCTTGAAATACACGGCA 57.554 34.783 0.00 0.00 35.79 5.69
199 202 6.763303 AAACATTTTCTTGAAATACACGGC 57.237 33.333 0.00 0.00 35.79 5.68
240 267 0.595588 TTTGGAATGCACGCGTGAAT 59.404 45.000 41.19 34.47 0.00 2.57
452 514 9.807921 ACACTTCTTTTTCCCTTTTCTATATGA 57.192 29.630 0.00 0.00 0.00 2.15
456 518 8.414003 GTGAACACTTCTTTTTCCCTTTTCTAT 58.586 33.333 0.00 0.00 0.00 1.98
458 520 6.210584 TGTGAACACTTCTTTTTCCCTTTTCT 59.789 34.615 6.51 0.00 0.00 2.52
459 521 6.394809 TGTGAACACTTCTTTTTCCCTTTTC 58.605 36.000 6.51 0.00 0.00 2.29
461 523 5.993748 TGTGAACACTTCTTTTTCCCTTT 57.006 34.783 6.51 0.00 0.00 3.11
462 524 7.839680 ATATGTGAACACTTCTTTTTCCCTT 57.160 32.000 6.51 0.00 0.00 3.95
463 525 7.839680 AATATGTGAACACTTCTTTTTCCCT 57.160 32.000 6.51 0.00 0.00 4.20
464 526 9.406828 GTAAATATGTGAACACTTCTTTTTCCC 57.593 33.333 6.51 0.00 0.00 3.97
465 527 9.959749 TGTAAATATGTGAACACTTCTTTTTCC 57.040 29.630 6.51 0.46 0.00 3.13
472 534 9.394477 GAGGTTTTGTAAATATGTGAACACTTC 57.606 33.333 6.51 0.00 0.00 3.01
482 544 7.487829 CCACCAAATCGAGGTTTTGTAAATATG 59.512 37.037 8.68 0.00 37.23 1.78
483 545 7.363443 CCCACCAAATCGAGGTTTTGTAAATAT 60.363 37.037 8.68 0.00 37.23 1.28
484 546 6.071840 CCCACCAAATCGAGGTTTTGTAAATA 60.072 38.462 8.68 0.00 37.23 1.40
485 547 5.279256 CCCACCAAATCGAGGTTTTGTAAAT 60.279 40.000 8.68 0.00 37.23 1.40
489 551 1.960689 CCCACCAAATCGAGGTTTTGT 59.039 47.619 8.68 0.00 37.23 2.83
490 552 2.235016 TCCCACCAAATCGAGGTTTTG 58.765 47.619 3.48 3.48 37.23 2.44
493 555 2.668144 TTTCCCACCAAATCGAGGTT 57.332 45.000 0.00 0.00 37.23 3.50
495 557 2.612212 CGTATTTCCCACCAAATCGAGG 59.388 50.000 0.00 0.00 0.00 4.63
496 558 3.063452 CACGTATTTCCCACCAAATCGAG 59.937 47.826 0.00 0.00 0.00 4.04
498 560 2.745281 ACACGTATTTCCCACCAAATCG 59.255 45.455 0.00 0.00 0.00 3.34
499 561 4.216687 TGAACACGTATTTCCCACCAAATC 59.783 41.667 6.62 0.00 0.00 2.17
500 562 4.145807 TGAACACGTATTTCCCACCAAAT 58.854 39.130 6.62 0.00 0.00 2.32
501 563 3.552875 TGAACACGTATTTCCCACCAAA 58.447 40.909 6.62 0.00 0.00 3.28
502 564 3.210232 TGAACACGTATTTCCCACCAA 57.790 42.857 6.62 0.00 0.00 3.67
505 567 8.603242 AATATAGATGAACACGTATTTCCCAC 57.397 34.615 6.62 0.23 0.00 4.61
540 602 8.690884 TGTGAACAATTCTTGAAATTACAGGAA 58.309 29.630 0.00 0.00 39.44 3.36
542 604 7.920151 TGTGTGAACAATTCTTGAAATTACAGG 59.080 33.333 0.00 0.00 0.00 4.00
543 605 8.854979 TGTGTGAACAATTCTTGAAATTACAG 57.145 30.769 0.00 0.00 0.00 2.74
545 607 8.856490 ACTGTGTGAACAATTCTTGAAATTAC 57.144 30.769 0.00 0.00 0.00 1.89
547 609 9.868277 TTAACTGTGTGAACAATTCTTGAAATT 57.132 25.926 0.00 0.00 0.00 1.82
550 612 9.352784 CTTTTAACTGTGTGAACAATTCTTGAA 57.647 29.630 0.00 0.00 0.00 2.69
552 614 8.909708 TCTTTTAACTGTGTGAACAATTCTTG 57.090 30.769 0.00 0.00 0.00 3.02
617 679 9.696917 CCTTCTTCTATTGCAAAAATACAAGTT 57.303 29.630 1.71 0.00 0.00 2.66
618 680 9.077885 TCCTTCTTCTATTGCAAAAATACAAGT 57.922 29.630 1.71 0.00 0.00 3.16
619 681 9.912634 TTCCTTCTTCTATTGCAAAAATACAAG 57.087 29.630 1.71 2.53 0.00 3.16
642 704 7.761704 GCCTCCTCTTTTTCTCATTTTTATTCC 59.238 37.037 0.00 0.00 0.00 3.01
643 705 8.526978 AGCCTCCTCTTTTTCTCATTTTTATTC 58.473 33.333 0.00 0.00 0.00 1.75
644 706 8.427902 AGCCTCCTCTTTTTCTCATTTTTATT 57.572 30.769 0.00 0.00 0.00 1.40
646 708 8.934023 TTAGCCTCCTCTTTTTCTCATTTTTA 57.066 30.769 0.00 0.00 0.00 1.52
652 714 7.016153 TGTAATTAGCCTCCTCTTTTTCTCA 57.984 36.000 0.00 0.00 0.00 3.27
653 715 7.770897 TCATGTAATTAGCCTCCTCTTTTTCTC 59.229 37.037 0.00 0.00 0.00 2.87
656 718 8.055181 TCATCATGTAATTAGCCTCCTCTTTTT 58.945 33.333 0.00 0.00 0.00 1.94
659 721 6.753913 TCATCATGTAATTAGCCTCCTCTT 57.246 37.500 0.00 0.00 0.00 2.85
661 723 5.406780 CGTTCATCATGTAATTAGCCTCCTC 59.593 44.000 0.00 0.00 0.00 3.71
662 724 5.300752 CGTTCATCATGTAATTAGCCTCCT 58.699 41.667 0.00 0.00 0.00 3.69
663 725 4.452455 CCGTTCATCATGTAATTAGCCTCC 59.548 45.833 0.00 0.00 0.00 4.30
664 726 4.083802 GCCGTTCATCATGTAATTAGCCTC 60.084 45.833 0.00 0.00 0.00 4.70
665 727 3.815401 GCCGTTCATCATGTAATTAGCCT 59.185 43.478 0.00 0.00 0.00 4.58
667 729 3.363970 CGGCCGTTCATCATGTAATTAGC 60.364 47.826 19.50 0.00 0.00 3.09
668 730 3.186409 CCGGCCGTTCATCATGTAATTAG 59.814 47.826 26.12 0.00 0.00 1.73
669 731 3.135225 CCGGCCGTTCATCATGTAATTA 58.865 45.455 26.12 0.00 0.00 1.40
670 732 1.946768 CCGGCCGTTCATCATGTAATT 59.053 47.619 26.12 0.00 0.00 1.40
671 733 1.140052 TCCGGCCGTTCATCATGTAAT 59.860 47.619 26.12 0.00 0.00 1.89
674 736 0.815213 CATCCGGCCGTTCATCATGT 60.815 55.000 26.12 0.00 0.00 3.21
675 737 1.509644 CCATCCGGCCGTTCATCATG 61.510 60.000 26.12 14.58 0.00 3.07
709 956 2.125552 CAAGCCATCTCGCACGGA 60.126 61.111 0.00 0.00 0.00 4.69
842 1095 1.202989 TGTTTTATGGGCTGGCACTGA 60.203 47.619 2.88 0.00 0.00 3.41
1113 1382 0.895530 CGTAGGTGCCTTCTCCAAGA 59.104 55.000 0.00 0.00 0.00 3.02
1164 1433 1.961277 CACGGCGACTTTCTTGCCT 60.961 57.895 16.62 0.00 46.71 4.75
1402 1671 4.096003 CATCACGCGGGTCCCCTT 62.096 66.667 8.89 0.00 0.00 3.95
1524 1793 0.179029 CCGACCCAAAGTCACCAACT 60.179 55.000 0.00 0.00 46.69 3.16
1872 2157 1.380403 TTGTTGAACCACCGGTGCTG 61.380 55.000 29.75 18.80 35.34 4.41
1888 2173 2.282462 CCGCTCCTTTGGGCTTGT 60.282 61.111 0.00 0.00 0.00 3.16
1904 2189 2.116125 ACAAAGCCAGGGTGCTCC 59.884 61.111 0.00 0.00 41.80 4.70
1995 2316 0.038251 CTAACTCAGTGTCAGCGGCA 60.038 55.000 1.45 0.00 0.00 5.69
1996 2317 1.355066 GCTAACTCAGTGTCAGCGGC 61.355 60.000 0.00 0.00 0.00 6.53
1997 2318 0.244994 AGCTAACTCAGTGTCAGCGG 59.755 55.000 0.00 0.00 37.32 5.52
1998 2319 2.071688 AAGCTAACTCAGTGTCAGCG 57.928 50.000 0.00 0.00 37.32 5.18
1999 2320 6.814146 AGTAATTAAGCTAACTCAGTGTCAGC 59.186 38.462 0.00 0.00 0.00 4.26
2000 2321 7.815068 ACAGTAATTAAGCTAACTCAGTGTCAG 59.185 37.037 0.00 0.00 0.00 3.51
2034 2360 7.438459 CCCTGCAACTAATTACAGACATACTAC 59.562 40.741 3.10 0.00 31.62 2.73
2035 2361 7.497595 CCCTGCAACTAATTACAGACATACTA 58.502 38.462 3.10 0.00 31.62 1.82
2036 2362 6.349300 CCCTGCAACTAATTACAGACATACT 58.651 40.000 3.10 0.00 31.62 2.12
2037 2363 5.007724 GCCCTGCAACTAATTACAGACATAC 59.992 44.000 3.10 0.00 31.62 2.39
2038 2364 5.123227 GCCCTGCAACTAATTACAGACATA 58.877 41.667 3.10 0.00 31.62 2.29
2039 2365 3.947834 GCCCTGCAACTAATTACAGACAT 59.052 43.478 3.10 0.00 31.62 3.06
2040 2366 3.343617 GCCCTGCAACTAATTACAGACA 58.656 45.455 3.10 0.00 31.62 3.41
2041 2367 2.683362 GGCCCTGCAACTAATTACAGAC 59.317 50.000 0.00 0.00 31.62 3.51
2042 2368 2.356741 GGGCCCTGCAACTAATTACAGA 60.357 50.000 17.04 0.00 31.62 3.41
2101 2435 6.849502 ACAGTAACTGAATCATTGATTGCTG 58.150 36.000 16.41 13.35 31.89 4.41
2148 2523 3.547746 TCGTTCAAACTTGGCCTTTAGT 58.452 40.909 3.32 1.66 0.00 2.24
2197 2746 6.008960 AGAAAGCTCAACCAGATTCAGAAAT 58.991 36.000 0.00 0.00 27.49 2.17
2226 2779 1.550524 AGCTTAGCAGATTCACACCGA 59.449 47.619 7.07 0.00 0.00 4.69
2231 2784 5.816777 AGATTCAGAAGCTTAGCAGATTCAC 59.183 40.000 7.07 0.00 46.28 3.18
2257 2810 4.161565 ACTTCACATCTGTATTTAGCCCGA 59.838 41.667 0.00 0.00 0.00 5.14
2259 2812 4.816925 GGACTTCACATCTGTATTTAGCCC 59.183 45.833 0.00 0.00 0.00 5.19
2261 2814 6.371548 TGTTGGACTTCACATCTGTATTTAGC 59.628 38.462 0.00 0.00 0.00 3.09
2262 2815 7.905604 TGTTGGACTTCACATCTGTATTTAG 57.094 36.000 0.00 0.00 0.00 1.85
2263 2816 7.095397 CGTTGTTGGACTTCACATCTGTATTTA 60.095 37.037 0.00 0.00 0.00 1.40
2286 2860 6.042143 AGACAATCAGCATTTGTTTTTCGTT 58.958 32.000 1.26 0.00 37.43 3.85
2288 2862 5.686841 TGAGACAATCAGCATTTGTTTTTCG 59.313 36.000 1.26 0.00 37.43 3.46
2305 2879 4.623932 ATCCAAGTTGCTAGTGAGACAA 57.376 40.909 0.00 0.00 0.00 3.18
2365 2962 7.555965 AGAAAAACTTGATTGCCTGTTTACTT 58.444 30.769 0.00 0.00 33.07 2.24
2407 3005 7.693952 TCTATTACCGCACATCAAAGAATTTC 58.306 34.615 0.00 0.00 35.03 2.17
2470 3069 1.087501 GCGGATGTTCCCTTTCTCAC 58.912 55.000 0.00 0.00 31.13 3.51
2474 3099 4.712122 TTTTATGCGGATGTTCCCTTTC 57.288 40.909 0.00 0.00 31.13 2.62
2502 3129 2.985282 TGCTGGGCCAAGAAAGCG 60.985 61.111 12.85 0.00 38.53 4.68


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

AutoCloner maintained by Alex Coulton.