Multiple sequence alignment - TraesCS3B01G530500

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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 TraesCS3B01G530500 chr3B 100.000 3585 0 0 1 3585 771535064 771531480 0.000000e+00 6621.0
1 TraesCS3B01G530500 chr3B 92.416 778 49 4 2808 3583 242875724 242874955 0.000000e+00 1101.0
2 TraesCS3B01G530500 chr3B 84.089 1037 149 12 1548 2572 771559058 771558026 0.000000e+00 987.0
3 TraesCS3B01G530500 chr3B 77.039 932 192 16 1599 2519 773876478 773875558 1.910000e-142 516.0
4 TraesCS3B01G530500 chr3B 77.812 658 123 17 1856 2500 802999026 802999673 5.610000e-103 385.0
5 TraesCS3B01G530500 chr3B 75.510 245 42 15 680 906 550989389 550989633 1.760000e-18 104.0
6 TraesCS3B01G530500 chr3D 93.372 1222 63 5 1501 2710 578243661 578242446 0.000000e+00 1792.0
7 TraesCS3B01G530500 chr3D 84.391 993 143 9 1548 2531 578260400 578259411 0.000000e+00 965.0
8 TraesCS3B01G530500 chr3D 86.181 673 45 9 826 1487 578245238 578244603 0.000000e+00 684.0
9 TraesCS3B01G530500 chr3D 78.041 929 182 18 1599 2519 579429346 579430260 1.870000e-157 566.0
10 TraesCS3B01G530500 chr3D 78.299 917 163 21 1583 2494 577969140 577970025 3.130000e-155 558.0
11 TraesCS3B01G530500 chr3D 90.237 379 37 0 6 384 578245977 578245599 2.490000e-136 496.0
12 TraesCS3B01G530500 chr3D 95.062 162 6 1 485 646 578245557 578245398 1.650000e-63 254.0
13 TraesCS3B01G530500 chr3D 97.368 38 1 0 784 821 578245298 578245261 8.310000e-07 65.8
14 TraesCS3B01G530500 chr3A 92.049 1220 86 7 1565 2779 713869073 713867860 0.000000e+00 1705.0
15 TraesCS3B01G530500 chr3A 90.224 1115 93 10 1557 2669 713850233 713849133 0.000000e+00 1441.0
16 TraesCS3B01G530500 chr3A 85.614 994 129 8 1548 2531 713931272 713930283 0.000000e+00 1031.0
17 TraesCS3B01G530500 chr3A 90.504 674 59 4 644 1315 713870331 713869661 0.000000e+00 885.0
18 TraesCS3B01G530500 chr3A 90.549 656 43 8 1 654 713870921 713870283 0.000000e+00 850.0
19 TraesCS3B01G530500 chr3A 78.710 930 177 13 1583 2506 713535484 713534570 5.120000e-168 601.0
20 TraesCS3B01G530500 chr3A 77.626 952 184 20 1584 2525 713623351 713622419 5.230000e-153 551.0
21 TraesCS3B01G530500 chr3A 82.857 245 21 8 1347 1575 713869496 713869257 2.180000e-47 200.0
22 TraesCS3B01G530500 chr3A 75.847 236 38 14 666 886 127062404 127062173 6.330000e-18 102.0
23 TraesCS3B01G530500 chr5B 95.561 811 33 3 2777 3585 676011898 676012707 0.000000e+00 1295.0
24 TraesCS3B01G530500 chr6B 95.303 809 37 1 2778 3585 49352600 49351792 0.000000e+00 1282.0
25 TraesCS3B01G530500 chr2B 94.307 808 43 3 2777 3583 211866154 211866959 0.000000e+00 1234.0
26 TraesCS3B01G530500 chr2B 78.327 263 38 13 661 906 403107739 403107999 6.200000e-33 152.0
27 TraesCS3B01G530500 chr4B 91.965 809 58 2 2778 3585 536815578 536814776 0.000000e+00 1127.0
28 TraesCS3B01G530500 chr4B 89.227 789 71 12 2802 3583 291769642 291768861 0.000000e+00 974.0
29 TraesCS3B01G530500 chr7D 89.835 787 75 5 2777 3560 250678791 250678007 0.000000e+00 1005.0
30 TraesCS3B01G530500 chr7D 78.750 240 30 18 669 890 339117063 339117299 1.340000e-29 141.0
31 TraesCS3B01G530500 chr2D 88.645 819 82 11 2769 3582 559241789 559240977 0.000000e+00 987.0
32 TraesCS3B01G530500 chr7A 87.675 787 82 14 2777 3556 39133548 39134326 0.000000e+00 902.0
33 TraesCS3B01G530500 chr7A 77.178 241 33 19 669 890 344677546 344677309 1.750000e-23 121.0
34 TraesCS3B01G530500 chr7B 78.603 229 30 18 680 890 284147452 284147679 2.250000e-27 134.0
35 TraesCS3B01G530500 chr2A 93.750 48 3 0 2778 2825 762708581 762708628 4.960000e-09 73.1


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 TraesCS3B01G530500 chr3B 771531480 771535064 3584 True 6621.00 6621 100.00000 1 3585 1 chr3B.!!$R2 3584
1 TraesCS3B01G530500 chr3B 242874955 242875724 769 True 1101.00 1101 92.41600 2808 3583 1 chr3B.!!$R1 775
2 TraesCS3B01G530500 chr3B 771558026 771559058 1032 True 987.00 987 84.08900 1548 2572 1 chr3B.!!$R3 1024
3 TraesCS3B01G530500 chr3B 773875558 773876478 920 True 516.00 516 77.03900 1599 2519 1 chr3B.!!$R4 920
4 TraesCS3B01G530500 chr3B 802999026 802999673 647 False 385.00 385 77.81200 1856 2500 1 chr3B.!!$F2 644
5 TraesCS3B01G530500 chr3D 578259411 578260400 989 True 965.00 965 84.39100 1548 2531 1 chr3D.!!$R1 983
6 TraesCS3B01G530500 chr3D 578242446 578245977 3531 True 658.36 1792 92.44400 6 2710 5 chr3D.!!$R2 2704
7 TraesCS3B01G530500 chr3D 579429346 579430260 914 False 566.00 566 78.04100 1599 2519 1 chr3D.!!$F2 920
8 TraesCS3B01G530500 chr3D 577969140 577970025 885 False 558.00 558 78.29900 1583 2494 1 chr3D.!!$F1 911
9 TraesCS3B01G530500 chr3A 713849133 713850233 1100 True 1441.00 1441 90.22400 1557 2669 1 chr3A.!!$R4 1112
10 TraesCS3B01G530500 chr3A 713930283 713931272 989 True 1031.00 1031 85.61400 1548 2531 1 chr3A.!!$R5 983
11 TraesCS3B01G530500 chr3A 713867860 713870921 3061 True 910.00 1705 88.98975 1 2779 4 chr3A.!!$R6 2778
12 TraesCS3B01G530500 chr3A 713534570 713535484 914 True 601.00 601 78.71000 1583 2506 1 chr3A.!!$R2 923
13 TraesCS3B01G530500 chr3A 713622419 713623351 932 True 551.00 551 77.62600 1584 2525 1 chr3A.!!$R3 941
14 TraesCS3B01G530500 chr5B 676011898 676012707 809 False 1295.00 1295 95.56100 2777 3585 1 chr5B.!!$F1 808
15 TraesCS3B01G530500 chr6B 49351792 49352600 808 True 1282.00 1282 95.30300 2778 3585 1 chr6B.!!$R1 807
16 TraesCS3B01G530500 chr2B 211866154 211866959 805 False 1234.00 1234 94.30700 2777 3583 1 chr2B.!!$F1 806
17 TraesCS3B01G530500 chr4B 536814776 536815578 802 True 1127.00 1127 91.96500 2778 3585 1 chr4B.!!$R2 807
18 TraesCS3B01G530500 chr4B 291768861 291769642 781 True 974.00 974 89.22700 2802 3583 1 chr4B.!!$R1 781
19 TraesCS3B01G530500 chr7D 250678007 250678791 784 True 1005.00 1005 89.83500 2777 3560 1 chr7D.!!$R1 783
20 TraesCS3B01G530500 chr2D 559240977 559241789 812 True 987.00 987 88.64500 2769 3582 1 chr2D.!!$R1 813
21 TraesCS3B01G530500 chr7A 39133548 39134326 778 False 902.00 902 87.67500 2777 3556 1 chr7A.!!$F1 779

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
909 933 0.444651 GGCACGCACGCATTTAGTAA 59.555 50.0 0.0 0.0 0.0 2.24 F
1000 1033 0.324738 AGAGCAGAGTCAATCGGGGA 60.325 55.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 3309 0.032813 CGGAGGGTGGGTAGGAGTTA 60.033 60.0 0.00 0.00 0.0 2.24 R
2665 3991 0.112995 AGAAGATGTTTGCCTGGCCA 59.887 50.0 17.53 4.71 0.0 5.36 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
101 102 9.862371 CTTAAGATATAGTAGTGCAATGGTAGG 57.138 37.037 0.00 0.00 0.00 3.18
107 108 1.754234 GTGCAATGGTAGGGCCCAG 60.754 63.158 27.56 5.36 38.07 4.45
126 127 6.239402 GGCCCAGATAATGCTTGTATTCAATT 60.239 38.462 0.00 0.00 32.82 2.32
168 169 9.202273 GGTCTCAAAATTTGCAACATATGTTTA 57.798 29.630 18.50 8.15 35.83 2.01
170 171 9.202273 TCTCAAAATTTGCAACATATGTTTACC 57.798 29.630 18.50 10.36 35.83 2.85
242 243 2.375174 TGTCAACAATAACTCAGGGGCT 59.625 45.455 0.00 0.00 0.00 5.19
260 261 4.697352 GGGGCTTATATGAATGTAGTGCAG 59.303 45.833 0.00 0.00 0.00 4.41
262 263 4.999950 GGCTTATATGAATGTAGTGCAGCT 59.000 41.667 0.00 0.00 0.00 4.24
276 277 7.083858 TGTAGTGCAGCTATTTGTCATTTTTC 58.916 34.615 0.00 0.00 31.50 2.29
319 320 1.329256 GCCGTCAGGAAGATAGGCTA 58.671 55.000 0.00 0.00 44.47 3.93
349 350 0.554792 CATGAATGGGGGAAGAGCCT 59.445 55.000 0.00 0.00 36.66 4.58
361 362 1.956477 GAAGAGCCTGCCAAGAAACAA 59.044 47.619 0.00 0.00 0.00 2.83
384 385 9.487790 ACAATTACAAATCCAATCGTGAAAATT 57.512 25.926 0.00 0.00 0.00 1.82
418 419 6.753913 ACATTTATATGCCAGAGAAGAGGA 57.246 37.500 0.00 0.00 35.03 3.71
474 475 9.823647 GACATTATATAGATACCAATGGACAGG 57.176 37.037 6.16 0.00 32.20 4.00
475 476 9.560860 ACATTATATAGATACCAATGGACAGGA 57.439 33.333 6.16 0.00 32.20 3.86
477 478 4.899352 ATAGATACCAATGGACAGGAGC 57.101 45.455 6.16 0.00 0.00 4.70
478 479 1.771255 AGATACCAATGGACAGGAGCC 59.229 52.381 6.16 0.00 0.00 4.70
479 480 1.771255 GATACCAATGGACAGGAGCCT 59.229 52.381 6.16 0.00 0.00 4.58
499 500 1.765314 TGCCAAGAATAGGAGAGGAGC 59.235 52.381 0.00 0.00 0.00 4.70
584 587 5.574830 TGTGCACTTTTGTAATTTCACACAC 59.425 36.000 19.41 0.00 30.03 3.82
607 610 9.062524 ACACCGAGAATCTATATCTATATCTGC 57.937 37.037 0.00 0.00 0.00 4.26
717 720 1.068333 CCAAACGGGCAGATTCAACTG 60.068 52.381 0.00 0.00 40.43 3.16
719 722 2.270352 AACGGGCAGATTCAACTGAA 57.730 45.000 0.00 0.00 39.94 3.02
733 736 1.813513 ACTGAAGTCGGCCATCAAAG 58.186 50.000 2.24 0.00 0.00 2.77
756 759 1.401539 GGCCAATTCAACGACTCAAGC 60.402 52.381 0.00 0.00 0.00 4.01
769 772 3.562505 GACTCAAGCTGCTTCAATTGTG 58.437 45.455 12.82 5.42 0.00 3.33
788 791 9.289303 CAATTGTGAGCGCTTAAAATATTTAGT 57.711 29.630 17.12 0.00 0.00 2.24
823 826 9.686683 ATACCATATCAAATATTAGCTCCAACC 57.313 33.333 0.00 0.00 0.00 3.77
890 914 3.748048 ACTGCCTAATATTAGCGTGCATG 59.252 43.478 19.04 15.94 29.45 4.06
909 933 0.444651 GGCACGCACGCATTTAGTAA 59.555 50.000 0.00 0.00 0.00 2.24
938 962 1.037030 ATACATGGTTGCCCAAGCCG 61.037 55.000 7.64 2.33 46.04 5.52
991 1024 1.476488 GTTGGAGGAGAGAGCAGAGTC 59.524 57.143 0.00 0.00 0.00 3.36
1000 1033 0.324738 AGAGCAGAGTCAATCGGGGA 60.325 55.000 0.00 0.00 0.00 4.81
1077 1110 4.516195 GCCGGAGTCTTCCTCGCC 62.516 72.222 5.05 0.00 41.67 5.54
1097 1130 2.171448 CCTCCCTTCCTTCAGGTATGTG 59.829 54.545 0.00 0.00 36.34 3.21
1129 1162 5.957842 AGGTGGTTTTGTATGTACATGTG 57.042 39.130 18.81 0.00 35.89 3.21
1130 1163 4.217550 AGGTGGTTTTGTATGTACATGTGC 59.782 41.667 18.81 8.01 35.89 4.57
1139 1172 7.770801 TTGTATGTACATGTGCTTAGATGTC 57.229 36.000 18.81 2.30 35.89 3.06
1199 1232 2.305052 CCCTTCTTTCCGGGTTCTACTT 59.695 50.000 0.00 0.00 35.65 2.24
1240 1273 2.223386 GCAGACCGTGTTTGTAAAGCAA 60.223 45.455 0.00 0.00 39.26 3.91
1260 1293 6.370593 AGCAATTGTATGTTCGTACTGTTTG 58.629 36.000 7.40 6.10 0.00 2.93
1274 1307 8.959734 TCGTACTGTTTGTAATATATGATCCG 57.040 34.615 0.00 0.00 32.25 4.18
1308 1341 6.150976 TGTTGGGTTCTACTATCAAAGCAATG 59.849 38.462 0.00 0.00 0.00 2.82
1320 1353 9.507280 ACTATCAAAGCAATGATAAAATTGTCG 57.493 29.630 11.24 2.60 40.71 4.35
1322 1355 6.918626 TCAAAGCAATGATAAAATTGTCGGA 58.081 32.000 0.00 0.00 39.33 4.55
1324 1357 8.681806 TCAAAGCAATGATAAAATTGTCGGATA 58.318 29.630 0.00 0.00 39.33 2.59
1325 1358 9.467258 CAAAGCAATGATAAAATTGTCGGATAT 57.533 29.630 0.00 0.00 39.33 1.63
1327 1360 8.169977 AGCAATGATAAAATTGTCGGATATGT 57.830 30.769 0.00 0.00 39.33 2.29
1339 1372 9.529325 AATTGTCGGATATGTATATTGATACCG 57.471 33.333 0.00 0.00 37.70 4.02
1341 1374 8.058667 TGTCGGATATGTATATTGATACCGTT 57.941 34.615 0.00 0.00 37.70 4.44
1342 1375 9.176460 TGTCGGATATGTATATTGATACCGTTA 57.824 33.333 0.00 0.00 37.70 3.18
1387 1553 6.989155 AGGTTTCATAACTATATCCACGGA 57.011 37.500 0.00 0.00 34.59 4.69
1423 1589 1.269309 CCACATCCCGCGAAAAACAAA 60.269 47.619 8.23 0.00 0.00 2.83
1424 1590 2.609244 CCACATCCCGCGAAAAACAAAT 60.609 45.455 8.23 0.00 0.00 2.32
1425 1591 3.056304 CACATCCCGCGAAAAACAAATT 58.944 40.909 8.23 0.00 0.00 1.82
1426 1592 4.230657 CACATCCCGCGAAAAACAAATTA 58.769 39.130 8.23 0.00 0.00 1.40
1427 1593 4.681942 CACATCCCGCGAAAAACAAATTAA 59.318 37.500 8.23 0.00 0.00 1.40
1482 1648 5.801350 AAGTATTGTGACATCGACCAATG 57.199 39.130 0.00 0.00 0.00 2.82
1496 1662 2.364972 CCAATGTATGGGAGGGGAAC 57.635 55.000 0.00 0.00 46.27 3.62
1497 1663 1.852965 CCAATGTATGGGAGGGGAACT 59.147 52.381 0.00 0.00 46.27 3.01
1498 1664 2.244769 CCAATGTATGGGAGGGGAACTT 59.755 50.000 0.00 0.00 46.27 2.66
1511 2605 5.105351 GGAGGGGAACTTTTGGTCAATATTG 60.105 44.000 9.29 9.29 38.05 1.90
1514 2608 4.929211 GGGAACTTTTGGTCAATATTGTGC 59.071 41.667 14.97 9.26 38.05 4.57
1519 2613 9.423061 GAACTTTTGGTCAATATTGTGCTTAAT 57.577 29.630 14.97 0.00 35.86 1.40
1532 2626 9.845740 ATATTGTGCTTAATGTACAGTGGATTA 57.154 29.630 5.98 0.00 41.99 1.75
1544 2640 7.995289 TGTACAGTGGATTATAGCCATTTTTG 58.005 34.615 0.00 0.00 37.81 2.44
1846 3141 1.550130 TAAAGCCCTACCACAGCGCT 61.550 55.000 2.64 2.64 40.21 5.92
1948 3243 4.223125 AACAAGGCCCTGGCAGCA 62.223 61.111 9.56 0.00 44.11 4.41
2004 3308 1.004277 GTGAGGTTCGACGTGCTCAG 61.004 60.000 0.00 0.00 0.00 3.35
2005 3309 1.286260 GAGGTTCGACGTGCTCAGT 59.714 57.895 0.00 0.00 0.00 3.41
2044 3348 4.980805 GCCGTGTTCGCTCACCCA 62.981 66.667 4.70 0.00 35.18 4.51
2146 3456 0.608035 GCAACCCGAGGGACATCAAA 60.608 55.000 16.26 0.00 38.96 2.69
2410 3720 3.983420 CCCAAGAAGCCTGGGCCA 61.983 66.667 5.85 5.85 43.17 5.36
2411 3721 2.361771 CCAAGAAGCCTGGGCCAT 59.638 61.111 6.72 0.00 43.17 4.40
2532 3842 1.027357 CCCATCAATTTCGCAGGAGG 58.973 55.000 0.00 0.00 0.00 4.30
2536 3846 2.113860 TCAATTTCGCAGGAGGAAGG 57.886 50.000 0.00 0.00 0.00 3.46
2596 3913 4.194640 GTGGACACTAGATTGATGCATGT 58.805 43.478 2.46 0.00 0.00 3.21
2598 3915 5.817296 GTGGACACTAGATTGATGCATGTAA 59.183 40.000 2.46 0.00 0.00 2.41
2603 3920 9.793252 GACACTAGATTGATGCATGTAAATTTT 57.207 29.630 2.46 0.00 0.00 1.82
2661 3987 9.507280 AAAAATAGTACGAAATCAATCATGCAG 57.493 29.630 0.00 0.00 0.00 4.41
2662 3988 4.542662 AGTACGAAATCAATCATGCAGC 57.457 40.909 0.00 0.00 0.00 5.25
2664 3990 3.853831 ACGAAATCAATCATGCAGCAA 57.146 38.095 0.00 0.00 0.00 3.91
2665 3991 4.380841 ACGAAATCAATCATGCAGCAAT 57.619 36.364 0.00 0.00 0.00 3.56
2666 3992 4.109766 ACGAAATCAATCATGCAGCAATG 58.890 39.130 0.00 0.00 0.00 2.82
2667 3993 3.489416 CGAAATCAATCATGCAGCAATGG 59.511 43.478 0.00 0.00 0.00 3.16
2668 3994 2.526304 ATCAATCATGCAGCAATGGC 57.474 45.000 0.00 0.00 41.61 4.40
2669 3995 0.462375 TCAATCATGCAGCAATGGCC 59.538 50.000 0.00 0.00 42.56 5.36
2670 3996 0.176910 CAATCATGCAGCAATGGCCA 59.823 50.000 8.56 8.56 42.56 5.36
2685 4011 1.260544 GGCCAGGCAAACATCTTCTT 58.739 50.000 15.19 0.00 0.00 2.52
2710 4036 8.630054 TTGCCTAATCTCTTCTCTATCTCTAC 57.370 38.462 0.00 0.00 0.00 2.59
2714 4040 9.396022 CCTAATCTCTTCTCTATCTCTACATCC 57.604 40.741 0.00 0.00 0.00 3.51
2715 4041 9.958180 CTAATCTCTTCTCTATCTCTACATCCA 57.042 37.037 0.00 0.00 0.00 3.41
2720 4046 7.402054 TCTTCTCTATCTCTACATCCATCTCC 58.598 42.308 0.00 0.00 0.00 3.71
2722 4048 7.096402 TCTCTATCTCTACATCCATCTCCAA 57.904 40.000 0.00 0.00 0.00 3.53
2735 4061 6.119240 TCCATCTCCAAAGACCATATCATC 57.881 41.667 0.00 0.00 33.32 2.92
2744 4070 5.378230 AAGACCATATCATCACACCATGT 57.622 39.130 0.00 0.00 0.00 3.21
2747 4073 5.366477 AGACCATATCATCACACCATGTGTA 59.634 40.000 8.71 0.00 45.65 2.90
2788 4114 8.215926 TCATTTTCACTCTTTACCGAAAAAGA 57.784 30.769 10.48 10.48 41.90 2.52
2833 4161 1.199097 GCAACGATCACCGAAACCAAT 59.801 47.619 0.00 0.00 41.76 3.16
2862 4190 0.884514 CACACAACACCACACCACAA 59.115 50.000 0.00 0.00 0.00 3.33
2928 4258 0.106719 CCACAACACCCCAACACTCT 60.107 55.000 0.00 0.00 0.00 3.24
2929 4259 1.308998 CACAACACCCCAACACTCTC 58.691 55.000 0.00 0.00 0.00 3.20
2957 4287 1.708341 ACAAATGAGCAACAAGGGCT 58.292 45.000 0.00 0.00 46.07 5.19
3074 4404 3.308705 GGGGAACGACACCGGAGT 61.309 66.667 9.46 6.23 40.78 3.85
3217 4547 1.221840 GAAGCCGAGCAAGGGATCA 59.778 57.895 0.00 0.00 0.00 2.92
3300 4631 2.281070 CCGAGCGGCCATAGCAAT 60.281 61.111 2.24 0.00 42.56 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 1.355720 GCATTATCTGGGCCCTACCAT 59.644 52.381 25.70 11.71 40.36 3.55
101 102 4.144297 TGAATACAAGCATTATCTGGGCC 58.856 43.478 0.00 0.00 0.00 5.80
126 127 3.887110 TGAGACCGACAACTCAGTAGAAA 59.113 43.478 0.00 0.00 38.08 2.52
229 230 7.335127 ACATTCATATAAGCCCCTGAGTTAT 57.665 36.000 0.00 0.00 0.00 1.89
242 243 9.559732 ACAAATAGCTGCACTACATTCATATAA 57.440 29.630 1.02 0.00 32.32 0.98
276 277 6.511767 GCATGACCGTTCTACATTAATGGAAG 60.512 42.308 19.37 15.15 36.64 3.46
319 320 4.017591 TCCCCCATTCATGTACACTTGATT 60.018 41.667 0.00 0.00 31.40 2.57
349 350 6.166984 TGGATTTGTAATTGTTTCTTGGCA 57.833 33.333 0.00 0.00 0.00 4.92
462 463 1.687612 CAGGCTCCTGTCCATTGGT 59.312 57.895 7.75 0.00 39.10 3.67
464 465 1.751927 GGCAGGCTCCTGTCCATTG 60.752 63.158 16.51 0.00 45.24 2.82
465 466 2.679716 GGCAGGCTCCTGTCCATT 59.320 61.111 16.51 0.00 45.24 3.16
471 472 1.476471 CCTATTCTTGGCAGGCTCCTG 60.476 57.143 11.47 11.47 46.15 3.86
472 473 0.842635 CCTATTCTTGGCAGGCTCCT 59.157 55.000 0.00 0.00 0.00 3.69
473 474 0.839946 TCCTATTCTTGGCAGGCTCC 59.160 55.000 0.00 0.00 0.00 4.70
474 475 1.765314 TCTCCTATTCTTGGCAGGCTC 59.235 52.381 0.00 0.00 0.00 4.70
475 476 1.767681 CTCTCCTATTCTTGGCAGGCT 59.232 52.381 0.00 0.00 0.00 4.58
476 477 1.202746 CCTCTCCTATTCTTGGCAGGC 60.203 57.143 0.00 0.00 0.00 4.85
477 478 2.368221 CTCCTCTCCTATTCTTGGCAGG 59.632 54.545 0.00 0.00 0.00 4.85
478 479 2.224257 GCTCCTCTCCTATTCTTGGCAG 60.224 54.545 0.00 0.00 0.00 4.85
479 480 1.765314 GCTCCTCTCCTATTCTTGGCA 59.235 52.381 0.00 0.00 0.00 4.92
480 481 1.071542 GGCTCCTCTCCTATTCTTGGC 59.928 57.143 0.00 0.00 0.00 4.52
481 482 2.368221 CAGGCTCCTCTCCTATTCTTGG 59.632 54.545 0.00 0.00 31.52 3.61
482 483 2.224257 GCAGGCTCCTCTCCTATTCTTG 60.224 54.545 0.00 0.00 31.52 3.02
483 484 2.046292 GCAGGCTCCTCTCCTATTCTT 58.954 52.381 0.00 0.00 31.52 2.52
499 500 3.940209 TTGTAATTGCTTCTTGGCAGG 57.060 42.857 0.00 0.00 43.39 4.85
697 700 1.068333 CAGTTGAATCTGCCCGTTTGG 60.068 52.381 0.00 0.00 37.09 3.28
698 701 1.879380 TCAGTTGAATCTGCCCGTTTG 59.121 47.619 0.00 0.00 35.63 2.93
702 705 1.734465 GACTTCAGTTGAATCTGCCCG 59.266 52.381 0.00 0.00 35.63 6.13
717 720 0.449388 CTGCTTTGATGGCCGACTTC 59.551 55.000 0.00 0.00 0.00 3.01
719 722 1.377725 CCTGCTTTGATGGCCGACT 60.378 57.895 0.00 0.00 0.00 4.18
733 736 0.169009 GAGTCGTTGAATTGGCCTGC 59.831 55.000 3.32 0.00 0.00 4.85
756 759 0.520404 AGCGCTCACAATTGAAGCAG 59.480 50.000 25.92 20.90 37.72 4.24
769 772 6.255215 TGCACACTAAATATTTTAAGCGCTC 58.745 36.000 12.06 0.00 0.00 5.03
890 914 0.444651 TTACTAAATGCGTGCGTGCC 59.555 50.000 0.00 0.00 0.00 5.01
938 962 7.013274 ATGTACTATTGGTGCATATCACAAACC 59.987 37.037 1.97 0.00 46.58 3.27
991 1024 2.058798 CGTATTCGACATCCCCGATTG 58.941 52.381 0.00 0.00 39.71 2.67
1024 1057 1.322442 AACACAGCAGAAAAGCCTCC 58.678 50.000 0.00 0.00 34.23 4.30
1077 1110 2.840651 ACACATACCTGAAGGAAGGGAG 59.159 50.000 2.62 0.00 42.11 4.30
1108 1141 4.217550 AGCACATGTACATACAAAACCACC 59.782 41.667 8.32 0.00 39.99 4.61
1207 1240 5.599999 ACACGGTCTGCTTTATAGAAGAT 57.400 39.130 0.00 0.00 38.36 2.40
1224 1257 5.918011 ACATACAATTGCTTTACAAACACGG 59.082 36.000 5.05 0.00 42.86 4.94
1271 1304 4.208746 AGAACCCAACAAAAATGTACGGA 58.791 39.130 0.00 0.00 0.00 4.69
1274 1307 9.005777 TGATAGTAGAACCCAACAAAAATGTAC 57.994 33.333 0.00 0.00 0.00 2.90
1281 1314 6.065374 TGCTTTGATAGTAGAACCCAACAAA 58.935 36.000 0.00 0.00 0.00 2.83
1286 1319 6.061022 TCATTGCTTTGATAGTAGAACCCA 57.939 37.500 0.00 0.00 0.00 4.51
1315 1348 8.058667 ACGGTATCAATATACATATCCGACAA 57.941 34.615 11.23 0.00 39.90 3.18
1316 1349 7.634671 ACGGTATCAATATACATATCCGACA 57.365 36.000 11.23 0.00 39.90 4.35
1333 1366 9.578439 GGTATCAATATACACCTTAACGGTATC 57.422 37.037 0.00 0.00 46.94 2.24
1338 1371 7.935338 AACGGTATCAATATACACCTTAACG 57.065 36.000 0.00 0.00 39.90 3.18
1341 1374 9.146586 ACCTTAACGGTATCAATATACACCTTA 57.853 33.333 0.00 0.00 46.73 2.69
1342 1375 8.026396 ACCTTAACGGTATCAATATACACCTT 57.974 34.615 0.00 0.00 46.73 3.50
1343 1376 7.607615 ACCTTAACGGTATCAATATACACCT 57.392 36.000 0.00 0.00 46.73 4.00
1393 1559 1.747206 GCGGGATGTGGCTATGAAACT 60.747 52.381 0.00 0.00 0.00 2.66
1423 1589 7.827236 TCTTCGTGTGGATATGAAACCTTTAAT 59.173 33.333 0.00 0.00 0.00 1.40
1424 1590 7.162761 TCTTCGTGTGGATATGAAACCTTTAA 58.837 34.615 0.00 0.00 0.00 1.52
1425 1591 6.703319 TCTTCGTGTGGATATGAAACCTTTA 58.297 36.000 0.00 0.00 0.00 1.85
1426 1592 5.556915 TCTTCGTGTGGATATGAAACCTTT 58.443 37.500 0.00 0.00 0.00 3.11
1427 1593 5.160607 TCTTCGTGTGGATATGAAACCTT 57.839 39.130 0.00 0.00 0.00 3.50
1482 1648 2.042569 ACCAAAAGTTCCCCTCCCATAC 59.957 50.000 0.00 0.00 0.00 2.39
1487 1653 2.375014 TTGACCAAAAGTTCCCCTCC 57.625 50.000 0.00 0.00 0.00 4.30
1488 1654 5.480422 ACAATATTGACCAAAAGTTCCCCTC 59.520 40.000 22.16 0.00 0.00 4.30
1489 1655 5.245977 CACAATATTGACCAAAAGTTCCCCT 59.754 40.000 22.16 0.00 0.00 4.79
1490 1656 5.478407 CACAATATTGACCAAAAGTTCCCC 58.522 41.667 22.16 0.00 0.00 4.81
1491 1657 4.929211 GCACAATATTGACCAAAAGTTCCC 59.071 41.667 22.16 0.00 0.00 3.97
1492 1658 5.783111 AGCACAATATTGACCAAAAGTTCC 58.217 37.500 22.16 0.00 0.00 3.62
1493 1659 8.810652 TTAAGCACAATATTGACCAAAAGTTC 57.189 30.769 22.16 0.00 0.00 3.01
1494 1660 9.206870 CATTAAGCACAATATTGACCAAAAGTT 57.793 29.630 22.16 5.68 0.00 2.66
1495 1661 8.367156 ACATTAAGCACAATATTGACCAAAAGT 58.633 29.630 22.16 9.14 0.00 2.66
1496 1662 8.761575 ACATTAAGCACAATATTGACCAAAAG 57.238 30.769 22.16 8.61 0.00 2.27
1497 1663 9.632807 GTACATTAAGCACAATATTGACCAAAA 57.367 29.630 22.16 10.29 0.00 2.44
1498 1664 8.797438 TGTACATTAAGCACAATATTGACCAAA 58.203 29.630 22.16 9.34 0.00 3.28
1511 2605 7.095187 GGCTATAATCCACTGTACATTAAGCAC 60.095 40.741 0.00 0.00 0.00 4.40
1514 2608 9.507329 AATGGCTATAATCCACTGTACATTAAG 57.493 33.333 0.00 0.00 36.26 1.85
1519 2613 7.613801 ACAAAAATGGCTATAATCCACTGTACA 59.386 33.333 0.00 0.00 36.26 2.90
1645 2935 1.274728 CTGTAGAGCTGCACCACTTCT 59.725 52.381 1.02 0.00 0.00 2.85
1915 3210 1.675641 GTTGAGGTTCCGCATGGCT 60.676 57.895 0.00 0.00 34.14 4.75
1962 3266 1.302511 GTGGACACCTTGATGGCGT 60.303 57.895 0.00 0.00 40.22 5.68
2004 3308 1.493861 GGAGGGTGGGTAGGAGTTAC 58.506 60.000 0.00 0.00 0.00 2.50
2005 3309 0.032813 CGGAGGGTGGGTAGGAGTTA 60.033 60.000 0.00 0.00 0.00 2.24
2044 3348 3.588277 GGCGATGTCGACCATGTAT 57.412 52.632 14.12 0.00 42.67 2.29
2146 3456 0.386478 GGAACGTCGCGTAGTTGAGT 60.386 55.000 21.94 3.16 39.99 3.41
2410 3720 0.734942 CGAACACGTACGCCTCCAAT 60.735 55.000 16.72 0.00 0.00 3.16
2411 3721 1.372004 CGAACACGTACGCCTCCAA 60.372 57.895 16.72 0.00 0.00 3.53
2603 3920 8.638873 TCTCTGCGAGGATATTATTTTGTTAGA 58.361 33.333 5.87 0.00 0.00 2.10
2645 3971 3.489416 CCATTGCTGCATGATTGATTTCG 59.511 43.478 1.84 0.00 0.00 3.46
2661 3987 0.741927 GATGTTTGCCTGGCCATTGC 60.742 55.000 17.53 18.07 0.00 3.56
2662 3988 0.899720 AGATGTTTGCCTGGCCATTG 59.100 50.000 17.53 0.98 0.00 2.82
2664 3990 1.188863 GAAGATGTTTGCCTGGCCAT 58.811 50.000 17.53 12.41 0.00 4.40
2665 3991 0.112995 AGAAGATGTTTGCCTGGCCA 59.887 50.000 17.53 4.71 0.00 5.36
2666 3992 1.260544 AAGAAGATGTTTGCCTGGCC 58.739 50.000 17.53 0.00 0.00 5.36
2667 3993 2.680577 CAAAGAAGATGTTTGCCTGGC 58.319 47.619 12.87 12.87 0.00 4.85
2685 4011 8.221251 TGTAGAGATAGAGAAGAGATTAGGCAA 58.779 37.037 0.00 0.00 0.00 4.52
2710 4036 5.872963 TGATATGGTCTTTGGAGATGGATG 58.127 41.667 0.00 0.00 33.70 3.51
2714 4040 6.204301 GTGTGATGATATGGTCTTTGGAGATG 59.796 42.308 0.00 0.00 33.70 2.90
2715 4041 6.294473 GTGTGATGATATGGTCTTTGGAGAT 58.706 40.000 0.00 0.00 33.70 2.75
2720 4046 5.591472 ACATGGTGTGATGATATGGTCTTTG 59.409 40.000 0.00 0.00 0.00 2.77
2722 4048 5.378230 ACATGGTGTGATGATATGGTCTT 57.622 39.130 0.00 0.00 0.00 3.01
2735 4061 6.371271 TGAGAACAATGTATACACATGGTGTG 59.629 38.462 19.31 8.44 46.69 3.82
2747 4073 9.071276 AGTGAAAATGAAGTGAGAACAATGTAT 57.929 29.630 0.00 0.00 0.00 2.29
2788 4114 7.176165 GCTTTATAATATAAAGCGGGGGAAACT 59.824 37.037 30.20 0.00 46.31 2.66
2833 4161 3.808726 GTGGTGTTGTGTGGTTATCGTTA 59.191 43.478 0.00 0.00 0.00 3.18
2862 4190 0.251386 TTGGGTGTGTTGTGTGGTGT 60.251 50.000 0.00 0.00 0.00 4.16
2928 4258 6.141560 TGTTGCTCATTTGTTGTATGTTGA 57.858 33.333 0.00 0.00 0.00 3.18
2929 4259 6.074195 CCTTGTTGCTCATTTGTTGTATGTTG 60.074 38.462 0.00 0.00 0.00 3.33
2957 4287 2.791655 TCTCCGACTACTTCAAGCTCA 58.208 47.619 0.00 0.00 0.00 4.26
3001 4331 0.748005 GAGCTCAGCCTCGTCTCTCT 60.748 60.000 9.40 0.00 0.00 3.10
3300 4631 2.574018 CGACTCAGGTGTGGGCTGA 61.574 63.158 0.00 0.00 0.00 4.26
3335 4666 0.949105 GTTGGTGGTAGTCACGCTGG 60.949 60.000 0.00 0.00 46.96 4.85
3490 4826 2.450320 CCTCTCCCCTGCCTGGATG 61.450 68.421 0.00 0.00 38.35 3.51
3498 4834 1.977293 GCTAGCAACCCTCTCCCCTG 61.977 65.000 10.63 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.