Multiple sequence alignment - TraesCS3A01G251200

Loading Multiple Alignment...

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 TraesCS3A01G251200 chr3A 100.000 3457 0 0 1 3457 470831017 470827561 0.000000e+00 6384.0
1 TraesCS3A01G251200 chr3B 91.076 3541 149 61 1 3457 451362881 451359424 0.000000e+00 4634.0
2 TraesCS3A01G251200 chr3D 94.144 2954 97 29 562 3457 352368680 352365745 0.000000e+00 4427.0
3 TraesCS3A01G251200 chr3D 91.111 495 22 10 1 485 352369291 352368809 0.000000e+00 651.0
4 TraesCS3A01G251200 chr2A 90.654 107 10 0 1267 1373 100826056 100825950 3.600000e-30 143.0
5 TraesCS3A01G251200 chr2B 90.566 106 10 0 1267 1372 152844328 152844223 1.290000e-29 141.0
6 TraesCS3A01G251200 chr2B 97.059 68 2 0 3383 3450 215840792 215840725 7.840000e-22 115.0
7 TraesCS3A01G251200 chr1B 85.294 136 20 0 1257 1392 109728735 109728870 1.290000e-29 141.0
8 TraesCS3A01G251200 chr7B 89.623 106 11 0 1267 1372 452961948 452962053 6.020000e-28 135.0
9 TraesCS3A01G251200 chr7A 85.827 127 18 0 1267 1393 486237273 486237147 6.020000e-28 135.0
10 TraesCS3A01G251200 chr4B 83.333 138 23 0 1257 1394 100576660 100576797 1.010000e-25 128.0
11 TraesCS3A01G251200 chr4D 82.609 138 24 0 1257 1394 68053411 68053548 4.690000e-24 122.0
12 TraesCS3A01G251200 chr1A 85.714 84 9 3 1040 1122 545000231 545000312 6.150000e-13 86.1


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 TraesCS3A01G251200 chr3A 470827561 470831017 3456 True 6384 6384 100.0000 1 3457 1 chr3A.!!$R1 3456
1 TraesCS3A01G251200 chr3B 451359424 451362881 3457 True 4634 4634 91.0760 1 3457 1 chr3B.!!$R1 3456
2 TraesCS3A01G251200 chr3D 352365745 352369291 3546 True 2539 4427 92.6275 1 3457 2 chr3D.!!$R1 3456

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
336 365 0.034574 TGGGCATGTAAGAACGGCAT 60.035 50.0 0.00 0.00 31.99 4.40 F
477 506 0.038021 TCCAAATGGTAGCTGCTGCA 59.962 50.0 19.24 0.88 37.86 4.41 F
532 599 0.250684 TTCCGCTCATGCAAACTGGA 60.251 50.0 0.00 0.00 39.64 3.86 F
973 1106 0.530650 CTGCGGTGAGTGTGAACTGT 60.531 55.0 0.00 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1159 1292 0.035881 TGGAACTGAAGCAGCAGAGG 59.964 55.000 12.11 0.0 39.20 3.69 R
1396 1530 0.619832 TCAAGCTGGAGCAGGAGGAT 60.620 55.000 0.65 0.0 45.16 3.24 R
1401 1536 0.963856 TGCATTCAAGCTGGAGCAGG 60.964 55.000 0.94 0.0 45.16 4.85 R
2722 2877 1.511305 CTCCGGCTGTACACATCGT 59.489 57.895 0.00 0.0 0.00 3.73 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
118 119 1.227205 CATGTCCTCGAGCCTGAGC 60.227 63.158 6.99 0.00 40.32 4.26
265 272 8.294341 TGCTTTCTGTATATATACAAAGTCGC 57.706 34.615 24.85 21.30 42.20 5.19
266 273 7.923878 TGCTTTCTGTATATATACAAAGTCGCA 59.076 33.333 24.85 22.74 42.20 5.10
267 274 8.761497 GCTTTCTGTATATATACAAAGTCGCAA 58.239 33.333 24.85 12.78 42.20 4.85
297 326 2.076100 TGCAGTCGCAGAGGTAAATTG 58.924 47.619 0.00 0.00 45.36 2.32
323 352 1.683365 GAAGGGTGCATGTGGGCAT 60.683 57.895 0.00 0.00 46.92 4.40
332 361 2.830772 CATGTGGGCATGTAAGAACG 57.169 50.000 0.00 0.00 45.48 3.95
333 362 1.401552 CATGTGGGCATGTAAGAACGG 59.598 52.381 0.00 0.00 45.48 4.44
336 365 0.034574 TGGGCATGTAAGAACGGCAT 60.035 50.000 0.00 0.00 31.99 4.40
339 368 3.924238 CATGTAAGAACGGCATGCC 57.076 52.632 27.67 27.67 34.47 4.40
356 385 4.730657 CATGCCAAAGAAGTAAAGAGCAG 58.269 43.478 0.00 0.00 31.70 4.24
357 386 3.149196 TGCCAAAGAAGTAAAGAGCAGG 58.851 45.455 0.00 0.00 0.00 4.85
365 394 3.704800 AGTAAAGAGCAGGGAAAGACC 57.295 47.619 0.00 0.00 38.08 3.85
374 403 2.166459 GCAGGGAAAGACCATTTAAGGC 59.834 50.000 0.00 0.00 41.20 4.35
410 439 8.811017 ACACATATATAGATGAAGGGTCAGAAG 58.189 37.037 14.15 0.00 37.14 2.85
477 506 0.038021 TCCAAATGGTAGCTGCTGCA 59.962 50.000 19.24 0.88 37.86 4.41
494 528 1.008194 CATGCATGCCATGTACCGC 60.008 57.895 14.93 0.00 45.05 5.68
495 529 1.453562 ATGCATGCCATGTACCGCA 60.454 52.632 16.68 0.00 39.79 5.69
496 530 1.449726 ATGCATGCCATGTACCGCAG 61.450 55.000 16.68 0.80 38.64 5.18
516 583 1.337167 GGCAGTGGCAGTGAAATTTCC 60.337 52.381 25.96 12.08 43.71 3.13
520 587 0.881118 TGGCAGTGAAATTTCCGCTC 59.119 50.000 15.48 9.68 0.00 5.03
528 595 3.121778 GTGAAATTTCCGCTCATGCAAAC 59.878 43.478 15.48 0.00 39.64 2.93
531 598 0.597568 TTTCCGCTCATGCAAACTGG 59.402 50.000 0.00 0.00 39.64 4.00
532 599 0.250684 TTCCGCTCATGCAAACTGGA 60.251 50.000 0.00 0.00 39.64 3.86
534 601 0.957395 CCGCTCATGCAAACTGGACT 60.957 55.000 0.00 0.00 39.64 3.85
536 603 2.076100 CGCTCATGCAAACTGGACTAA 58.924 47.619 0.00 0.00 39.64 2.24
537 604 2.679837 CGCTCATGCAAACTGGACTAAT 59.320 45.455 0.00 0.00 39.64 1.73
540 607 4.156556 GCTCATGCAAACTGGACTAATCAA 59.843 41.667 0.00 0.00 39.41 2.57
544 616 4.203226 TGCAAACTGGACTAATCAACACA 58.797 39.130 0.00 0.00 0.00 3.72
545 617 4.036262 TGCAAACTGGACTAATCAACACAC 59.964 41.667 0.00 0.00 0.00 3.82
547 619 5.751680 CAAACTGGACTAATCAACACACTG 58.248 41.667 0.00 0.00 0.00 3.66
552 624 3.058914 GGACTAATCAACACACTGCACAC 60.059 47.826 0.00 0.00 0.00 3.82
562 634 0.887836 CACTGCACACTCACAGGCAT 60.888 55.000 0.00 0.00 38.25 4.40
564 636 1.583495 CTGCACACTCACAGGCATGG 61.583 60.000 2.31 0.00 35.45 3.66
569 641 0.812811 CACTCACAGGCATGGATCGG 60.813 60.000 2.31 0.00 0.00 4.18
570 642 0.977627 ACTCACAGGCATGGATCGGA 60.978 55.000 2.31 0.00 0.00 4.55
668 748 4.410400 GGGGTGGAGCGTGGAAGG 62.410 72.222 0.00 0.00 0.00 3.46
824 929 1.449778 GGGCTCGACAGGTTTAGGC 60.450 63.158 0.00 0.00 0.00 3.93
870 975 0.543277 TCTGCCTGCCCTTAGATGTG 59.457 55.000 0.00 0.00 0.00 3.21
970 1103 2.607892 GCCTGCGGTGAGTGTGAAC 61.608 63.158 0.00 0.00 0.00 3.18
971 1104 1.069765 CCTGCGGTGAGTGTGAACT 59.930 57.895 0.00 0.00 0.00 3.01
972 1105 1.224069 CCTGCGGTGAGTGTGAACTG 61.224 60.000 0.00 0.00 0.00 3.16
973 1106 0.530650 CTGCGGTGAGTGTGAACTGT 60.531 55.000 0.00 0.00 0.00 3.55
990 1123 5.009710 TGAACTGTGTAGTAGTTGAGTGAGG 59.990 44.000 0.00 0.00 38.42 3.86
991 1124 4.726583 ACTGTGTAGTAGTTGAGTGAGGA 58.273 43.478 0.00 0.00 34.74 3.71
1136 1269 1.625818 AGTCCCAAGACAAGCTGGTAG 59.374 52.381 0.00 0.00 46.15 3.18
1142 1275 1.741770 GACAAGCTGGTAGGTGCGG 60.742 63.158 0.00 0.00 0.00 5.69
1143 1276 2.436646 CAAGCTGGTAGGTGCGGG 60.437 66.667 0.00 0.00 0.00 6.13
1144 1277 3.717294 AAGCTGGTAGGTGCGGGG 61.717 66.667 0.00 0.00 0.00 5.73
1189 1322 0.610174 TCAGTTCCACCAGCTAGCTG 59.390 55.000 33.58 33.58 43.26 4.24
1396 1530 2.039348 GGTGCTAGGGAACAGGTAAACA 59.961 50.000 0.00 0.00 0.00 2.83
1401 1536 4.683671 GCTAGGGAACAGGTAAACATCCTC 60.684 50.000 0.00 0.00 32.37 3.71
1456 1594 3.214328 CCCTACCCTACATGCAAATCAC 58.786 50.000 0.00 0.00 0.00 3.06
1489 1627 1.745653 GCTGTAACTTCATTCCCCTGC 59.254 52.381 0.00 0.00 0.00 4.85
1502 1645 0.957395 CCCCTGCACACATGACAGTC 60.957 60.000 0.00 0.00 31.73 3.51
1536 1679 1.602041 TGCATGGCCTACACGCAAA 60.602 52.632 3.32 0.00 46.44 3.68
1559 1702 7.667043 AAGCGAGTAGTTTGAAATCACATTA 57.333 32.000 0.00 0.00 0.00 1.90
1560 1703 7.295952 AGCGAGTAGTTTGAAATCACATTAG 57.704 36.000 0.00 0.00 0.00 1.73
1561 1704 5.960105 GCGAGTAGTTTGAAATCACATTAGC 59.040 40.000 0.00 0.00 0.00 3.09
1562 1705 6.183360 GCGAGTAGTTTGAAATCACATTAGCT 60.183 38.462 0.00 0.00 0.00 3.32
1603 1746 1.962807 TGAAAGGGACACAAATGGCAG 59.037 47.619 0.00 0.00 34.30 4.85
1618 1761 2.294979 TGGCAGCAGATTGAGCTAATG 58.705 47.619 0.00 0.00 41.14 1.90
1845 1990 5.886960 AACTACTCCAGTACGTACGAAAT 57.113 39.130 24.41 1.48 36.04 2.17
1846 1991 5.886960 ACTACTCCAGTACGTACGAAATT 57.113 39.130 24.41 1.05 34.98 1.82
1847 1992 5.634896 ACTACTCCAGTACGTACGAAATTG 58.365 41.667 24.41 15.29 34.98 2.32
1848 1993 3.248266 ACTCCAGTACGTACGAAATTGC 58.752 45.455 24.41 2.58 0.00 3.56
1888 2033 8.135529 AGTTAATTTTCTCTTCCAAAAGAACCG 58.864 33.333 0.00 0.00 40.95 4.44
1956 2103 1.881973 ACGCACTAACTCGGAGTTACA 59.118 47.619 23.14 9.42 39.51 2.41
2006 2153 3.501911 ATTCTGGATGGGGCGGGG 61.502 66.667 0.00 0.00 0.00 5.73
2420 2567 1.877367 GTCCGTCGACAGCTTCTCT 59.123 57.895 17.16 0.00 38.99 3.10
2496 2643 3.054779 TGGGTAGGTGTATGTATGGCT 57.945 47.619 0.00 0.00 0.00 4.75
2518 2665 5.344743 TTGATCTAGTAGTTGGCTTCCTG 57.655 43.478 0.00 0.00 0.00 3.86
2675 2830 2.112928 ATGCTTGTCCGTGTGCCA 59.887 55.556 0.00 0.00 0.00 4.92
2680 2835 0.588252 CTTGTCCGTGTGCCAAAGAG 59.412 55.000 0.00 0.00 0.00 2.85
2722 2877 9.758651 CTACACCACATATAGTTTTGTATGCTA 57.241 33.333 0.00 0.00 33.16 3.49
2790 2945 1.965935 TGCATGACGGTGGGAATATG 58.034 50.000 0.00 0.00 0.00 1.78
2826 2983 3.545633 GCTAGCTGCGCAAATTATACAC 58.454 45.455 13.05 0.00 0.00 2.90
2930 3087 8.018520 CGGTGCTAAACATACTGAAATTGTTAA 58.981 33.333 0.00 0.00 33.44 2.01
2951 3108 5.483685 AAATCTGTCAGGTGTAAGCAGTA 57.516 39.130 0.00 0.00 36.26 2.74
2952 3109 5.683876 AATCTGTCAGGTGTAAGCAGTAT 57.316 39.130 0.00 0.00 36.26 2.12
2953 3110 4.720649 TCTGTCAGGTGTAAGCAGTATC 57.279 45.455 0.00 0.00 36.26 2.24
3004 3169 0.979709 TCTCCCACCCTCATCAGCTG 60.980 60.000 7.63 7.63 0.00 4.24
3071 3236 1.270625 TGAAACCTCTGTTGGTAGGCG 60.271 52.381 0.00 0.00 39.83 5.52
3077 3242 0.606604 TCTGTTGGTAGGCGAAGGTC 59.393 55.000 0.00 0.00 0.00 3.85
3164 3331 1.206115 GCAAAACCGCAACCGTTCAG 61.206 55.000 0.00 0.00 0.00 3.02
3170 3337 4.389576 GCAACCGTTCAGCTGCCG 62.390 66.667 9.47 13.50 0.00 5.69
3174 3341 2.892425 CCGTTCAGCTGCCGATCC 60.892 66.667 22.17 1.69 0.00 3.36
3379 3546 1.206578 CACTCGGACGCGCAAATTT 59.793 52.632 5.73 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.059800 GCCTTTCCGTATTTATCAGCGTC 60.060 47.826 0.00 0.00 0.00 5.19
18 19 3.564225 GGTGGCCTTTCCGTATTTATCAG 59.436 47.826 3.32 0.00 37.80 2.90
118 119 1.271656 CAAAGGGCTGCAAGAAGGAAG 59.728 52.381 0.50 0.00 34.07 3.46
119 120 1.331214 CAAAGGGCTGCAAGAAGGAA 58.669 50.000 0.50 0.00 34.07 3.36
120 121 1.181098 GCAAAGGGCTGCAAGAAGGA 61.181 55.000 0.50 0.00 42.17 3.36
121 122 1.291272 GCAAAGGGCTGCAAGAAGG 59.709 57.895 0.50 0.00 42.17 3.46
213 220 1.064505 CCGCGTGCATTCATTCATTCT 59.935 47.619 4.92 0.00 0.00 2.40
318 347 0.381801 CATGCCGTTCTTACATGCCC 59.618 55.000 0.00 0.00 35.24 5.36
323 352 1.539388 CTTTGGCATGCCGTTCTTACA 59.461 47.619 30.87 8.74 39.42 2.41
332 361 3.674410 GCTCTTTACTTCTTTGGCATGCC 60.674 47.826 30.54 30.54 0.00 4.40
333 362 3.057315 TGCTCTTTACTTCTTTGGCATGC 60.057 43.478 9.90 9.90 0.00 4.06
336 365 3.149196 CCTGCTCTTTACTTCTTTGGCA 58.851 45.455 0.00 0.00 0.00 4.92
339 368 5.765182 TCTTTCCCTGCTCTTTACTTCTTTG 59.235 40.000 0.00 0.00 0.00 2.77
356 385 4.207955 CCTAGCCTTAAATGGTCTTTCCC 58.792 47.826 0.00 0.00 34.77 3.97
357 386 4.207955 CCCTAGCCTTAAATGGTCTTTCC 58.792 47.826 0.00 0.00 0.00 3.13
374 403 5.921962 TCTATATATGTGTGCTGCCCTAG 57.078 43.478 0.00 0.00 0.00 3.02
424 453 6.844696 TTCGTCAAGAAGATATGTAATGGC 57.155 37.500 0.00 0.00 34.26 4.40
425 454 9.045223 TCAATTCGTCAAGAAGATATGTAATGG 57.955 33.333 0.00 0.00 42.92 3.16
477 506 1.449726 CTGCGGTACATGGCATGCAT 61.450 55.000 26.70 11.46 38.69 3.96
482 516 3.974835 CTGCCTGCGGTACATGGCA 62.975 63.158 15.85 15.85 44.88 4.92
492 526 4.994471 TCACTGCCACTGCCTGCG 62.994 66.667 0.00 0.00 36.33 5.18
493 527 1.530013 ATTTCACTGCCACTGCCTGC 61.530 55.000 0.00 0.00 36.33 4.85
494 528 0.963962 AATTTCACTGCCACTGCCTG 59.036 50.000 0.00 0.00 36.33 4.85
495 529 1.615392 GAAATTTCACTGCCACTGCCT 59.385 47.619 13.40 0.00 36.33 4.75
496 530 1.337167 GGAAATTTCACTGCCACTGCC 60.337 52.381 19.49 0.00 36.33 4.85
497 531 1.666888 CGGAAATTTCACTGCCACTGC 60.667 52.381 19.49 0.00 38.26 4.40
498 532 1.666888 GCGGAAATTTCACTGCCACTG 60.667 52.381 19.49 0.00 32.93 3.66
500 534 0.598065 AGCGGAAATTTCACTGCCAC 59.402 50.000 19.49 0.00 38.95 5.01
501 535 0.881118 GAGCGGAAATTTCACTGCCA 59.119 50.000 19.49 0.00 38.95 4.92
516 583 1.725641 TAGTCCAGTTTGCATGAGCG 58.274 50.000 0.00 0.00 46.23 5.03
520 587 5.156355 GTGTTGATTAGTCCAGTTTGCATG 58.844 41.667 0.00 0.00 0.00 4.06
528 595 3.187227 GTGCAGTGTGTTGATTAGTCCAG 59.813 47.826 0.00 0.00 0.00 3.86
531 598 3.809832 AGTGTGCAGTGTGTTGATTAGTC 59.190 43.478 0.00 0.00 0.00 2.59
532 599 3.808728 AGTGTGCAGTGTGTTGATTAGT 58.191 40.909 0.00 0.00 0.00 2.24
534 601 3.559655 GTGAGTGTGCAGTGTGTTGATTA 59.440 43.478 0.00 0.00 0.00 1.75
536 603 1.942657 GTGAGTGTGCAGTGTGTTGAT 59.057 47.619 0.00 0.00 0.00 2.57
537 604 1.338579 TGTGAGTGTGCAGTGTGTTGA 60.339 47.619 0.00 0.00 0.00 3.18
540 607 0.462581 CCTGTGAGTGTGCAGTGTGT 60.463 55.000 0.00 0.00 0.00 3.72
544 616 0.887836 CATGCCTGTGAGTGTGCAGT 60.888 55.000 0.00 0.00 37.12 4.40
545 617 1.583495 CCATGCCTGTGAGTGTGCAG 61.583 60.000 0.00 0.00 37.12 4.41
547 619 0.679002 ATCCATGCCTGTGAGTGTGC 60.679 55.000 0.00 0.00 0.00 4.57
552 624 0.249784 CTCCGATCCATGCCTGTGAG 60.250 60.000 0.00 0.00 0.00 3.51
562 634 4.147449 CTGTGCGCCTCCGATCCA 62.147 66.667 4.18 0.00 36.29 3.41
564 636 1.589196 GTACTGTGCGCCTCCGATC 60.589 63.158 4.18 0.00 36.29 3.69
569 641 0.038159 ACTCTTGTACTGTGCGCCTC 60.038 55.000 4.18 0.00 0.00 4.70
570 642 0.393077 AACTCTTGTACTGTGCGCCT 59.607 50.000 4.18 0.00 0.00 5.52
668 748 3.733960 GCGAGGGGCGTTTTGGTC 61.734 66.667 0.00 0.00 43.41 4.02
691 771 0.966370 AGGCGTGACTGGACTAGACC 60.966 60.000 4.09 4.09 0.00 3.85
728 808 0.514691 CAAAAGTGAGTGGCTCGAGC 59.485 55.000 29.38 29.38 41.14 5.03
824 929 0.893727 CACGGGGAGGAAAAGTTGGG 60.894 60.000 0.00 0.00 0.00 4.12
870 975 1.725066 GCAATGCAATGCAATGGCC 59.275 52.632 22.79 5.40 44.92 5.36
958 1091 3.454371 ACTACACAGTTCACACTCACC 57.546 47.619 0.00 0.00 0.00 4.02
970 1103 5.004448 TCTCCTCACTCAACTACTACACAG 58.996 45.833 0.00 0.00 0.00 3.66
971 1104 4.981812 TCTCCTCACTCAACTACTACACA 58.018 43.478 0.00 0.00 0.00 3.72
972 1105 5.247084 TCTCTCCTCACTCAACTACTACAC 58.753 45.833 0.00 0.00 0.00 2.90
973 1106 5.492895 CTCTCTCCTCACTCAACTACTACA 58.507 45.833 0.00 0.00 0.00 2.74
990 1123 1.406860 GGTGCCCCATCTCCTCTCTC 61.407 65.000 0.00 0.00 0.00 3.20
991 1124 1.383803 GGTGCCCCATCTCCTCTCT 60.384 63.158 0.00 0.00 0.00 3.10
1035 1168 3.403558 GACCACAGGCCCCTCCTC 61.404 72.222 0.00 0.00 45.52 3.71
1147 1280 1.880340 GCAGAGGTCGAATCCGCAG 60.880 63.158 2.97 0.00 35.37 5.18
1156 1289 0.320247 AACTGAAGCAGCAGAGGTCG 60.320 55.000 12.11 0.00 39.20 4.79
1157 1290 1.437625 GAACTGAAGCAGCAGAGGTC 58.562 55.000 12.11 0.00 39.20 3.85
1158 1291 0.036022 GGAACTGAAGCAGCAGAGGT 59.964 55.000 12.11 0.00 39.20 3.85
1159 1292 0.035881 TGGAACTGAAGCAGCAGAGG 59.964 55.000 12.11 0.00 39.20 3.69
1396 1530 0.619832 TCAAGCTGGAGCAGGAGGAT 60.620 55.000 0.65 0.00 45.16 3.24
1401 1536 0.963856 TGCATTCAAGCTGGAGCAGG 60.964 55.000 0.94 0.00 45.16 4.85
1489 1627 5.119743 CACAGATAAGTGACTGTCATGTGTG 59.880 44.000 22.47 20.61 44.07 3.82
1502 1645 1.713597 TGCAGACGCACAGATAAGTG 58.286 50.000 0.00 0.00 45.36 3.16
1534 1677 6.560253 ATGTGATTTCAAACTACTCGCTTT 57.440 33.333 0.00 0.00 0.00 3.51
1536 1679 6.183360 GCTAATGTGATTTCAAACTACTCGCT 60.183 38.462 0.00 0.00 0.00 4.93
1540 1683 8.043710 AGCTAGCTAATGTGATTTCAAACTACT 58.956 33.333 17.69 0.00 0.00 2.57
1546 1689 5.649395 AGCAAGCTAGCTAATGTGATTTCAA 59.351 36.000 19.70 0.00 44.50 2.69
1547 1690 5.188434 AGCAAGCTAGCTAATGTGATTTCA 58.812 37.500 19.70 0.00 44.50 2.69
1548 1691 5.557893 CGAGCAAGCTAGCTAATGTGATTTC 60.558 44.000 19.70 9.92 46.75 2.17
1560 1703 1.663135 CCTTTTCTCGAGCAAGCTAGC 59.337 52.381 6.62 6.62 0.00 3.42
1561 1704 3.238108 TCCTTTTCTCGAGCAAGCTAG 57.762 47.619 7.81 0.00 0.00 3.42
1562 1705 3.678056 TTCCTTTTCTCGAGCAAGCTA 57.322 42.857 7.81 1.15 0.00 3.32
1603 1746 3.788333 TTTGGCATTAGCTCAATCTGC 57.212 42.857 0.00 0.00 41.70 4.26
1618 1761 1.550659 CGCACAGCACACATTTTGGC 61.551 55.000 0.00 0.00 0.00 4.52
1772 1915 1.831736 CAGAGGAAGGGATGTTACCGT 59.168 52.381 0.00 0.00 0.00 4.83
1848 1993 8.485976 AGAAAATTAACTAGTAGCTCTGCAAG 57.514 34.615 0.00 0.00 0.00 4.01
1888 2033 7.849804 ATACATGTTTGGTGTCAGATTAGAC 57.150 36.000 2.30 0.00 38.99 2.59
1939 2086 4.557690 CGACATTGTAACTCCGAGTTAGTG 59.442 45.833 19.30 18.56 40.95 2.74
1956 2103 6.801575 ACAAATCTGTACCAAAAACGACATT 58.198 32.000 0.00 0.00 32.54 2.71
2006 2153 4.849329 GCAGCTGCGATGCCTTGC 62.849 66.667 25.23 0.00 37.73 4.01
2263 2410 4.925861 GGCAGCTCCGATCAGCCC 62.926 72.222 1.57 0.00 40.65 5.19
2496 2643 5.023452 TCAGGAAGCCAACTACTAGATCAA 58.977 41.667 0.00 0.00 0.00 2.57
2675 2830 7.604545 GTGTAGCTAATCAGAAGTTTCCTCTTT 59.395 37.037 0.00 0.00 0.00 2.52
2680 2835 5.351740 GTGGTGTAGCTAATCAGAAGTTTCC 59.648 44.000 0.00 0.00 0.00 3.13
2722 2877 1.511305 CTCCGGCTGTACACATCGT 59.489 57.895 0.00 0.00 0.00 3.73
2790 2945 3.986572 CAGCTAGCTCATGCATACACTAC 59.013 47.826 16.15 0.00 42.74 2.73
2826 2983 5.532557 TGATAATGCTTGACGATAGGAGTG 58.467 41.667 0.00 0.00 43.77 3.51
2880 3037 2.681706 ACTGCACGAGTGAATCTTCAG 58.318 47.619 7.50 6.14 37.98 3.02
2930 3087 5.187772 TGATACTGCTTACACCTGACAGATT 59.812 40.000 3.32 0.00 32.67 2.40
2951 3108 9.897744 CAGTTGACACTGTTTATTTGTTATGAT 57.102 29.630 0.00 0.00 44.96 2.45
2974 3139 1.620822 GGTGGGAGATGTTTTGCAGT 58.379 50.000 0.00 0.00 0.00 4.40
3004 3169 9.589111 TCCAAACACCTTTATTTTTACTTTCAC 57.411 29.630 0.00 0.00 0.00 3.18
3071 3236 2.586357 GCCTGCCGATCGACCTTC 60.586 66.667 18.66 0.00 0.00 3.46
3077 3242 3.257561 CAAGACGCCTGCCGATCG 61.258 66.667 8.51 8.51 41.02 3.69
3119 3286 2.547211 CTGGTCAGTTTCTGCAGACAAG 59.453 50.000 18.03 6.58 32.79 3.16
3120 3287 2.170397 TCTGGTCAGTTTCTGCAGACAA 59.830 45.455 18.03 11.31 30.01 3.18
3301 3468 0.871163 CTTGTGCGGTTGTGCCTTTG 60.871 55.000 0.00 0.00 34.25 2.77
3363 3530 1.226018 GGAAATTTGCGCGTCCGAG 60.226 57.895 8.43 0.00 36.29 4.63
3364 3531 2.682876 GGGAAATTTGCGCGTCCGA 61.683 57.895 8.43 0.00 36.29 4.55
3379 3546 1.000233 AGCCGCAAATGGAATGGGA 60.000 52.632 0.00 0.00 32.93 4.37


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

AutoCloner maintained by Alex Coulton.