Multiple sequence alignment - TraesCS2D01G159300

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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 TraesCS2D01G159300 chr2D 100.000 2809 0 0 1 2809 102647873 102645065 0.000000e+00 5188
1 TraesCS2D01G159300 chr2D 79.058 616 68 36 944 1542 102728627 102728056 1.590000e-97 366
2 TraesCS2D01G159300 chr2B 88.416 2089 140 52 1 2035 153896535 153894495 0.000000e+00 2423
3 TraesCS2D01G159300 chr2B 92.913 635 39 3 2044 2677 153894183 153893554 0.000000e+00 918
4 TraesCS2D01G159300 chr2B 90.610 426 39 1 2344 2768 692398118 692398543 5.250000e-157 564
5 TraesCS2D01G159300 chr2B 85.546 339 28 14 1207 1542 153907765 153907445 4.480000e-88 335
6 TraesCS2D01G159300 chr2A 87.332 1563 82 41 528 2026 101825590 101824080 0.000000e+00 1683
7 TraesCS2D01G159300 chr2A 86.831 486 52 5 1 483 101826058 101825582 1.480000e-147 532
8 TraesCS2D01G159300 chr2A 88.747 391 36 4 2420 2809 101801080 101800697 3.280000e-129 472
9 TraesCS2D01G159300 chr2A 87.589 419 29 12 2048 2465 101801479 101801083 5.480000e-127 464
10 TraesCS2D01G159300 chr2A 86.136 339 26 14 1207 1542 101840177 101839857 2.070000e-91 346
11 TraesCS2D01G159300 chr5D 85.757 674 39 29 1040 1709 432892929 432892309 0.000000e+00 660
12 TraesCS2D01G159300 chr4A 88.489 278 18 8 1204 1476 358874271 358874539 9.700000e-85 324
13 TraesCS2D01G159300 chr4A 85.859 198 10 9 1512 1709 358879846 358880025 7.940000e-46 195
14 TraesCS2D01G159300 chr1B 90.270 185 18 0 1240 1424 588239655 588239839 2.800000e-60 243
15 TraesCS2D01G159300 chr1B 81.452 248 21 14 1460 1707 588239832 588240054 2.220000e-41 180


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 TraesCS2D01G159300 chr2D 102645065 102647873 2808 True 5188.0 5188 100.0000 1 2809 1 chr2D.!!$R1 2808
1 TraesCS2D01G159300 chr2D 102728056 102728627 571 True 366.0 366 79.0580 944 1542 1 chr2D.!!$R2 598
2 TraesCS2D01G159300 chr2B 153893554 153896535 2981 True 1670.5 2423 90.6645 1 2677 2 chr2B.!!$R2 2676
3 TraesCS2D01G159300 chr2A 101824080 101826058 1978 True 1107.5 1683 87.0815 1 2026 2 chr2A.!!$R3 2025
4 TraesCS2D01G159300 chr2A 101800697 101801479 782 True 468.0 472 88.1680 2048 2809 2 chr2A.!!$R2 761
5 TraesCS2D01G159300 chr5D 432892309 432892929 620 True 660.0 660 85.7570 1040 1709 1 chr5D.!!$R1 669

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
304 310 0.179089 CGCACATTCCTCCTCCTCTG 60.179 60.0 0.0 0.0 0.0 3.35 F
1199 1286 0.249120 TCGGAAATGATGTGACGGCT 59.751 50.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 1267 0.24912 AGCCGTCACATCATTTCCGA 59.751 50.0 0.0 0.0 0.0 4.55 R
2037 2156 0.24912 TGCCTGGATTGGTGACGTAG 59.751 55.0 0.0 0.0 0.0 3.51 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
54 56 2.556622 GGACATCGGTTTCACCAATGTT 59.443 45.455 1.06 0.00 42.96 2.71
61 63 4.513692 TCGGTTTCACCAATGTTTGTCTAG 59.486 41.667 0.00 0.00 38.47 2.43
116 118 9.944663 TTATCATAATTCTTAACGGTCAATTGC 57.055 29.630 0.00 0.00 0.00 3.56
117 119 7.384439 TCATAATTCTTAACGGTCAATTGCA 57.616 32.000 0.00 0.00 0.00 4.08
118 120 7.247728 TCATAATTCTTAACGGTCAATTGCAC 58.752 34.615 0.00 0.10 0.00 4.57
119 121 5.446143 AATTCTTAACGGTCAATTGCACA 57.554 34.783 0.00 0.00 0.00 4.57
120 122 3.889196 TCTTAACGGTCAATTGCACAC 57.111 42.857 0.00 0.00 0.00 3.82
121 123 3.206964 TCTTAACGGTCAATTGCACACA 58.793 40.909 0.00 0.00 0.00 3.72
160 162 5.468658 ACCTCTTACTATGTCTTATGCCCT 58.531 41.667 0.00 0.00 0.00 5.19
164 167 6.936279 TCTTACTATGTCTTATGCCCTATGC 58.064 40.000 0.00 0.00 41.77 3.14
166 169 7.893833 TCTTACTATGTCTTATGCCCTATGCTA 59.106 37.037 0.00 0.00 42.00 3.49
173 176 6.318648 TGTCTTATGCCCTATGCTAAGTTTTG 59.681 38.462 0.00 0.00 42.00 2.44
177 180 6.796785 ATGCCCTATGCTAAGTTTTGAAAT 57.203 33.333 0.00 0.00 42.00 2.17
215 218 1.745264 CTCCATCCTCCTCGGCTTC 59.255 63.158 0.00 0.00 0.00 3.86
238 241 2.490217 CGATCGTTCCGCCTCTGT 59.510 61.111 7.03 0.00 0.00 3.41
274 278 1.004862 CTTCCCACCTCCTCCCTTTTC 59.995 57.143 0.00 0.00 0.00 2.29
286 292 3.368531 CCTCCCTTTTCCTTCTCACTACG 60.369 52.174 0.00 0.00 0.00 3.51
296 302 2.941453 TCTCACTACGCACATTCCTC 57.059 50.000 0.00 0.00 0.00 3.71
304 310 0.179089 CGCACATTCCTCCTCCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
305 311 0.908198 GCACATTCCTCCTCCTCTGT 59.092 55.000 0.00 0.00 0.00 3.41
309 315 2.314549 ACATTCCTCCTCCTCTGTCTCT 59.685 50.000 0.00 0.00 0.00 3.10
310 316 2.818751 TTCCTCCTCCTCTGTCTCTC 57.181 55.000 0.00 0.00 0.00 3.20
321 333 1.527433 CTGTCTCTCCGCCACTGTCA 61.527 60.000 0.00 0.00 0.00 3.58
326 338 2.031012 TCCGCCACTGTCAAGCTG 59.969 61.111 0.00 0.00 0.00 4.24
357 369 3.381272 CCACACACAACAAATCCTTCACT 59.619 43.478 0.00 0.00 0.00 3.41
411 423 4.492160 GTCGTCGCCATCTCGCCA 62.492 66.667 0.00 0.00 0.00 5.69
421 433 2.213499 CCATCTCGCCATTGACCTAAC 58.787 52.381 0.00 0.00 0.00 2.34
425 437 0.687920 TCGCCATTGACCTAACCACA 59.312 50.000 0.00 0.00 0.00 4.17
428 440 2.084546 GCCATTGACCTAACCACAGTC 58.915 52.381 0.00 0.00 0.00 3.51
463 476 3.423154 CCACCTTCCGCTCGTTGC 61.423 66.667 0.00 0.00 38.57 4.17
486 499 3.324207 GGCTTGTCCCTCTTCGTTT 57.676 52.632 0.00 0.00 0.00 3.60
487 500 1.157585 GGCTTGTCCCTCTTCGTTTC 58.842 55.000 0.00 0.00 0.00 2.78
500 513 3.254903 TCTTCGTTTCATCTTCCGACTCA 59.745 43.478 0.00 0.00 0.00 3.41
501 514 3.868757 TCGTTTCATCTTCCGACTCAT 57.131 42.857 0.00 0.00 0.00 2.90
502 515 3.770666 TCGTTTCATCTTCCGACTCATC 58.229 45.455 0.00 0.00 0.00 2.92
503 516 3.444034 TCGTTTCATCTTCCGACTCATCT 59.556 43.478 0.00 0.00 0.00 2.90
507 520 3.017442 TCATCTTCCGACTCATCTTCGT 58.983 45.455 0.00 0.00 34.56 3.85
508 521 3.065510 TCATCTTCCGACTCATCTTCGTC 59.934 47.826 0.00 0.00 34.56 4.20
512 525 3.221834 CGACTCATCTTCGTCGGTC 57.778 57.895 4.09 0.00 46.61 4.79
514 527 1.931841 CGACTCATCTTCGTCGGTCTA 59.068 52.381 4.09 0.00 46.61 2.59
517 530 3.810941 GACTCATCTTCGTCGGTCTATCT 59.189 47.826 0.00 0.00 0.00 1.98
519 532 3.139850 TCATCTTCGTCGGTCTATCTCC 58.860 50.000 0.00 0.00 0.00 3.71
521 534 0.953003 CTTCGTCGGTCTATCTCCCC 59.047 60.000 0.00 0.00 0.00 4.81
522 535 0.256752 TTCGTCGGTCTATCTCCCCA 59.743 55.000 0.00 0.00 0.00 4.96
541 562 1.074395 CCCCTCCCCCTTCTCCTAC 60.074 68.421 0.00 0.00 0.00 3.18
543 564 1.604592 CCCTCCCCCTTCTCCTACCT 61.605 65.000 0.00 0.00 0.00 3.08
550 571 2.026169 CCCCTTCTCCTACCTTTCCAAC 60.026 54.545 0.00 0.00 0.00 3.77
557 578 0.323629 CTACCTTTCCAACCCAGCGA 59.676 55.000 0.00 0.00 0.00 4.93
577 598 5.584649 AGCGATCGAAATTTCCTATGTTTCA 59.415 36.000 21.57 0.00 32.75 2.69
578 599 5.677178 GCGATCGAAATTTCCTATGTTTCAC 59.323 40.000 21.57 0.00 32.75 3.18
580 601 7.464358 CGATCGAAATTTCCTATGTTTCACTT 58.536 34.615 10.26 0.00 32.75 3.16
629 650 9.394767 GTAATATCAAAATTTTGGGCCAGATTT 57.605 29.630 26.45 18.68 38.66 2.17
634 655 8.108551 TCAAAATTTTGGGCCAGATTTAAATG 57.891 30.769 26.45 18.33 38.66 2.32
637 658 8.703378 AAATTTTGGGCCAGATTTAAATGAAA 57.297 26.923 21.39 10.58 0.00 2.69
644 665 7.038445 TGGGCCAGATTTAAATGAAATTCAAGA 60.038 33.333 0.00 0.00 37.90 3.02
645 666 7.989170 GGGCCAGATTTAAATGAAATTCAAGAT 59.011 33.333 4.39 0.00 37.90 2.40
666 691 9.030301 CAAGATAAATTTAAATTTGGCCTACCG 57.970 33.333 28.45 14.00 38.90 4.02
706 735 6.491403 GCATGGAGATCAAAATAATAGTGGGT 59.509 38.462 0.00 0.00 0.00 4.51
752 792 5.848786 GCGCAGAGCTAAGCTAAATTATAC 58.151 41.667 0.30 0.00 39.88 1.47
753 793 5.635700 GCGCAGAGCTAAGCTAAATTATACT 59.364 40.000 0.30 0.00 39.88 2.12
754 794 6.807230 GCGCAGAGCTAAGCTAAATTATACTA 59.193 38.462 0.30 0.00 39.88 1.82
755 795 7.201367 GCGCAGAGCTAAGCTAAATTATACTAC 60.201 40.741 0.30 0.00 39.88 2.73
756 796 8.024285 CGCAGAGCTAAGCTAAATTATACTACT 58.976 37.037 8.09 0.00 39.88 2.57
884 929 2.013563 GCTCCGATCCAACTTGCATGA 61.014 52.381 6.60 0.00 0.00 3.07
962 1016 3.184541 CAATAATCGAACTTCGTCCGGT 58.815 45.455 10.88 0.00 41.35 5.28
1033 1091 1.164411 CTCACAGCTCACTCGTCTCT 58.836 55.000 0.00 0.00 0.00 3.10
1054 1112 1.601477 CCGGCCGGTTGGTTAACTT 60.601 57.895 36.64 0.00 36.99 2.66
1055 1113 0.321475 CCGGCCGGTTGGTTAACTTA 60.321 55.000 36.64 0.00 36.99 2.24
1091 1175 0.829333 AGCTAGCTCACATGGGTCTG 59.171 55.000 12.68 0.00 0.00 3.51
1181 1268 4.131088 GGCGACGGTGAGGAGGTC 62.131 72.222 0.00 0.00 0.00 3.85
1184 1271 2.360852 GACGGTGAGGAGGTCGGA 60.361 66.667 0.00 0.00 0.00 4.55
1185 1272 1.975407 GACGGTGAGGAGGTCGGAA 60.975 63.158 0.00 0.00 0.00 4.30
1186 1273 1.530013 GACGGTGAGGAGGTCGGAAA 61.530 60.000 0.00 0.00 0.00 3.13
1187 1274 0.903454 ACGGTGAGGAGGTCGGAAAT 60.903 55.000 0.00 0.00 0.00 2.17
1188 1275 0.460284 CGGTGAGGAGGTCGGAAATG 60.460 60.000 0.00 0.00 0.00 2.32
1189 1276 0.902531 GGTGAGGAGGTCGGAAATGA 59.097 55.000 0.00 0.00 0.00 2.57
1190 1277 1.486726 GGTGAGGAGGTCGGAAATGAT 59.513 52.381 0.00 0.00 0.00 2.45
1191 1278 2.555199 GTGAGGAGGTCGGAAATGATG 58.445 52.381 0.00 0.00 0.00 3.07
1192 1279 2.093447 GTGAGGAGGTCGGAAATGATGT 60.093 50.000 0.00 0.00 0.00 3.06
1193 1280 2.093500 TGAGGAGGTCGGAAATGATGTG 60.093 50.000 0.00 0.00 0.00 3.21
1194 1281 2.168521 GAGGAGGTCGGAAATGATGTGA 59.831 50.000 0.00 0.00 0.00 3.58
1195 1282 2.093447 AGGAGGTCGGAAATGATGTGAC 60.093 50.000 0.00 0.00 0.00 3.67
1196 1283 1.927174 GAGGTCGGAAATGATGTGACG 59.073 52.381 0.00 0.00 0.00 4.35
1197 1284 1.006832 GGTCGGAAATGATGTGACGG 58.993 55.000 0.00 0.00 0.00 4.79
1198 1285 0.373716 GTCGGAAATGATGTGACGGC 59.626 55.000 0.00 0.00 0.00 5.68
1199 1286 0.249120 TCGGAAATGATGTGACGGCT 59.751 50.000 0.00 0.00 0.00 5.52
1200 1287 0.374758 CGGAAATGATGTGACGGCTG 59.625 55.000 0.00 0.00 0.00 4.85
1204 1291 4.758251 TGATGTGACGGCTGCGGG 62.758 66.667 11.99 0.00 0.00 6.13
1205 1292 4.760047 GATGTGACGGCTGCGGGT 62.760 66.667 11.99 3.37 0.00 5.28
1565 1671 3.374367 CCTGCTGATCATCTCAACAACTG 59.626 47.826 0.00 0.00 29.83 3.16
1612 1718 2.289547 TCATCAACTCATCATGCATGCG 59.710 45.455 22.25 14.93 31.70 4.73
1840 1953 3.268013 ACTTGCGATTCGTTTTTGGAG 57.732 42.857 8.03 0.00 0.00 3.86
1841 1954 2.875933 ACTTGCGATTCGTTTTTGGAGA 59.124 40.909 8.03 0.00 0.00 3.71
1878 1994 3.043713 TGCTGTACGTGCTGCTGC 61.044 61.111 29.26 17.07 40.20 5.25
1885 2001 1.128692 GTACGTGCTGCTGCCTTTAAG 59.871 52.381 13.47 0.00 38.71 1.85
1886 2002 0.535102 ACGTGCTGCTGCCTTTAAGT 60.535 50.000 13.47 0.00 38.71 2.24
1904 2020 7.486551 CCTTTAAGTTTGTTTCATTGACGTTCA 59.513 33.333 0.00 0.00 0.00 3.18
1907 2023 5.331902 AGTTTGTTTCATTGACGTTCAGTG 58.668 37.500 0.00 0.00 35.70 3.66
1997 2113 0.731514 ACGTCACGTAATGGCACGAG 60.732 55.000 0.00 0.00 44.69 4.18
2031 2150 2.793946 CCCGCTGCACATGCTAAC 59.206 61.111 5.31 0.00 42.66 2.34
2035 2154 1.135315 CCGCTGCACATGCTAACAATT 60.135 47.619 5.31 0.00 42.66 2.32
2036 2155 2.097304 CCGCTGCACATGCTAACAATTA 59.903 45.455 5.31 0.00 42.66 1.40
2037 2156 3.100817 CGCTGCACATGCTAACAATTAC 58.899 45.455 5.31 0.00 42.66 1.89
2039 2158 4.033932 CGCTGCACATGCTAACAATTACTA 59.966 41.667 5.31 0.00 42.66 1.82
2040 2159 5.266242 GCTGCACATGCTAACAATTACTAC 58.734 41.667 5.31 0.00 42.66 2.73
2042 2161 4.932799 TGCACATGCTAACAATTACTACGT 59.067 37.500 5.31 0.00 42.66 3.57
2053 2475 5.175859 ACAATTACTACGTCACCAATCCAG 58.824 41.667 0.00 0.00 0.00 3.86
2085 2507 9.898152 AATTCTCTGTTATTTCTAAGAAGGAGG 57.102 33.333 0.00 0.00 0.00 4.30
2098 2520 4.545208 AGAAGGAGGTCTTTCTAACTGC 57.455 45.455 2.67 0.00 39.99 4.40
2099 2521 4.164204 AGAAGGAGGTCTTTCTAACTGCT 58.836 43.478 2.67 0.00 39.99 4.24
2160 2583 2.590114 AACACCAGACGGGGCCTAC 61.590 63.158 0.84 0.00 40.67 3.18
2171 2594 2.682494 GGCCTACCCGTCTCACCA 60.682 66.667 0.00 0.00 0.00 4.17
2189 2612 4.943705 TCACCATGTTTTCCTTCTGCTATC 59.056 41.667 0.00 0.00 0.00 2.08
2373 2796 2.158623 ACCACTTGCAGTTCTTCATCCA 60.159 45.455 0.00 0.00 0.00 3.41
2377 2800 3.567164 ACTTGCAGTTCTTCATCCAGTTG 59.433 43.478 0.00 0.00 0.00 3.16
2389 2812 5.246981 TCATCCAGTTGAAGAATCCACTT 57.753 39.130 0.00 0.00 29.53 3.16
2417 2840 4.507710 CAGTATGCCACTACACAACATCT 58.492 43.478 0.00 0.00 34.98 2.90
2432 2903 1.032794 CATCTACCGGCACAGAGCTA 58.967 55.000 0.00 0.00 44.79 3.32
2455 2926 2.499205 TCGATGGCGATCACCACC 59.501 61.111 4.15 0.00 44.17 4.61
2459 2930 2.298158 GATGGCGATCACCACCGAGT 62.298 60.000 4.15 0.00 44.17 4.18
2464 2935 1.888018 GATCACCACCGAGTTCCGA 59.112 57.895 0.00 0.00 41.76 4.55
2467 2938 1.183030 TCACCACCGAGTTCCGATGT 61.183 55.000 0.00 0.00 41.76 3.06
2470 2941 2.100631 CACCGAGTTCCGATGTGGC 61.101 63.158 0.00 0.00 41.76 5.01
2678 3149 3.866379 AATCAGCCGGCCACTGCAA 62.866 57.895 26.15 0.00 40.13 4.08
2681 3152 3.297620 AGCCGGCCACTGCAAAAG 61.298 61.111 26.15 0.00 40.13 2.27
2683 3154 2.956987 CCGGCCACTGCAAAAGAG 59.043 61.111 2.24 0.00 40.13 2.85
2694 3165 1.291272 CAAAAGAGCAGGCCAAGGC 59.709 57.895 5.01 5.60 41.06 4.35
2700 3171 3.618750 GCAGGCCAAGGCAGCAAA 61.619 61.111 18.83 0.00 44.11 3.68
2714 3185 4.159135 AGGCAGCAAAATGATCTTGGTTAG 59.841 41.667 0.00 0.00 32.37 2.34
2717 3188 5.678107 GCAGCAAAATGATCTTGGTTAGGAG 60.678 44.000 0.00 0.00 32.37 3.69
2718 3189 4.952335 AGCAAAATGATCTTGGTTAGGAGG 59.048 41.667 0.00 0.00 30.56 4.30
2720 3191 5.509498 CAAAATGATCTTGGTTAGGAGGGA 58.491 41.667 0.00 0.00 0.00 4.20
2722 3193 2.119495 TGATCTTGGTTAGGAGGGAGC 58.881 52.381 0.00 0.00 0.00 4.70
2736 3207 1.144503 AGGGAGCATTTGATAGGCCAG 59.855 52.381 5.01 0.00 0.00 4.85
2737 3208 1.133668 GGGAGCATTTGATAGGCCAGT 60.134 52.381 5.01 0.00 0.00 4.00
2744 3215 2.113860 TTGATAGGCCAGTTGCTCAC 57.886 50.000 5.01 0.00 40.92 3.51
2750 3221 2.472029 AGGCCAGTTGCTCACTACTAT 58.528 47.619 5.01 0.00 40.92 2.12
2751 3222 2.840651 AGGCCAGTTGCTCACTACTATT 59.159 45.455 5.01 0.00 40.92 1.73
2757 3228 6.631016 CCAGTTGCTCACTACTATTGAGTAA 58.369 40.000 3.71 3.71 41.61 2.24
2762 3233 7.462571 TGCTCACTACTATTGAGTAACTGAA 57.537 36.000 5.57 0.00 42.26 3.02
2764 3235 8.531982 TGCTCACTACTATTGAGTAACTGAAAT 58.468 33.333 5.57 0.00 42.26 2.17
2765 3236 8.812329 GCTCACTACTATTGAGTAACTGAAATG 58.188 37.037 5.57 0.00 42.26 2.32
2775 3246 8.725405 TTGAGTAACTGAAATGTTAGTGTTGA 57.275 30.769 0.00 0.00 36.53 3.18
2776 3247 8.725405 TGAGTAACTGAAATGTTAGTGTTGAA 57.275 30.769 0.00 0.00 36.53 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.065803 CGATGTCCCTATTTGTCTGTAAACATT 59.934 37.037 0.00 0.00 0.00 2.71
21 22 2.838202 ACCGATGTCCCTATTTGTCTGT 59.162 45.455 0.00 0.00 0.00 3.41
54 56 3.211045 GGGTGCAAAAGTGTCTAGACAA 58.789 45.455 26.74 7.11 43.77 3.18
61 63 2.572290 ACTAGTGGGTGCAAAAGTGTC 58.428 47.619 0.00 0.00 0.00 3.67
118 120 8.967635 AAGAGGTCTTACCATGTCTGCATGTG 62.968 46.154 6.80 1.97 41.95 3.21
119 121 7.040049 AAGAGGTCTTACCATGTCTGCATGT 62.040 44.000 6.80 0.00 41.95 3.21
120 122 4.624843 AAGAGGTCTTACCATGTCTGCATG 60.625 45.833 0.00 0.96 41.95 4.06
121 123 3.110705 AGAGGTCTTACCATGTCTGCAT 58.889 45.455 0.00 0.00 41.95 3.96
274 278 2.093973 AGGAATGTGCGTAGTGAGAAGG 60.094 50.000 0.00 0.00 0.00 3.46
286 292 0.908198 ACAGAGGAGGAGGAATGTGC 59.092 55.000 0.00 0.00 0.00 4.57
296 302 2.124693 GGCGGAGAGACAGAGGAGG 61.125 68.421 0.00 0.00 0.00 4.30
304 310 0.389166 CTTGACAGTGGCGGAGAGAC 60.389 60.000 0.00 0.00 0.00 3.36
305 311 1.967535 CTTGACAGTGGCGGAGAGA 59.032 57.895 0.00 0.00 0.00 3.10
309 315 2.031012 CAGCTTGACAGTGGCGGA 59.969 61.111 0.00 0.00 0.00 5.54
310 316 3.052082 CCAGCTTGACAGTGGCGG 61.052 66.667 0.00 0.00 0.00 6.13
326 338 4.514585 TGTGTGTGGTGGCACCCC 62.515 66.667 32.61 23.29 37.50 4.95
357 369 4.303794 ACTAGTGGTAATAAGCCCATCCA 58.696 43.478 0.00 0.00 32.32 3.41
411 423 3.181458 ACAACGACTGTGGTTAGGTCAAT 60.181 43.478 7.88 0.00 36.69 2.57
421 433 1.202533 AGGAGTCAACAACGACTGTGG 60.203 52.381 0.00 0.00 46.26 4.17
428 440 1.070134 TGGAAGGAGGAGTCAACAACG 59.930 52.381 0.00 0.00 0.00 4.10
486 499 3.017442 ACGAAGATGAGTCGGAAGATGA 58.983 45.455 0.00 0.00 45.19 2.92
487 500 3.367607 GACGAAGATGAGTCGGAAGATG 58.632 50.000 0.00 0.00 45.19 2.90
500 513 2.506444 GGGAGATAGACCGACGAAGAT 58.494 52.381 0.00 0.00 0.00 2.40
501 514 1.476471 GGGGAGATAGACCGACGAAGA 60.476 57.143 0.00 0.00 0.00 2.87
502 515 0.953003 GGGGAGATAGACCGACGAAG 59.047 60.000 0.00 0.00 0.00 3.79
503 516 0.256752 TGGGGAGATAGACCGACGAA 59.743 55.000 0.00 0.00 0.00 3.85
507 520 1.232216 GGGTGGGGAGATAGACCGA 59.768 63.158 0.00 0.00 0.00 4.69
508 521 1.837499 GGGGTGGGGAGATAGACCG 60.837 68.421 0.00 0.00 0.00 4.79
511 524 1.675936 GGGAGGGGTGGGGAGATAGA 61.676 65.000 0.00 0.00 0.00 1.98
512 525 1.152008 GGGAGGGGTGGGGAGATAG 60.152 68.421 0.00 0.00 0.00 2.08
514 527 4.124126 GGGGAGGGGTGGGGAGAT 62.124 72.222 0.00 0.00 0.00 2.75
519 532 4.371231 AGAAGGGGGAGGGGTGGG 62.371 72.222 0.00 0.00 0.00 4.61
521 534 1.898190 TAGGAGAAGGGGGAGGGGTG 61.898 65.000 0.00 0.00 0.00 4.61
522 535 1.551964 TAGGAGAAGGGGGAGGGGT 60.552 63.158 0.00 0.00 0.00 4.95
541 562 1.369091 CGATCGCTGGGTTGGAAAGG 61.369 60.000 0.26 0.00 0.00 3.11
543 564 0.035598 TTCGATCGCTGGGTTGGAAA 59.964 50.000 11.09 0.00 0.00 3.13
550 571 1.668419 AGGAAATTTCGATCGCTGGG 58.332 50.000 11.09 0.00 0.00 4.45
664 689 3.119955 CCATGCTTGCATGATCTTATCGG 60.120 47.826 30.12 11.57 34.66 4.18
666 691 5.001874 TCTCCATGCTTGCATGATCTTATC 58.998 41.667 30.12 0.00 34.66 1.75
706 735 3.132824 TCTCATCTCCATGCGAGCTAAAA 59.867 43.478 6.38 0.00 38.62 1.52
752 792 0.875908 ACGCCACGCATGCATAGTAG 60.876 55.000 19.57 6.51 0.00 2.57
753 793 0.386113 TACGCCACGCATGCATAGTA 59.614 50.000 19.57 10.91 0.00 1.82
754 794 0.875908 CTACGCCACGCATGCATAGT 60.876 55.000 19.57 11.89 0.00 2.12
755 795 0.875908 ACTACGCCACGCATGCATAG 60.876 55.000 19.57 10.77 0.00 2.23
756 796 0.386113 TACTACGCCACGCATGCATA 59.614 50.000 19.57 0.00 0.00 3.14
757 797 0.249868 ATACTACGCCACGCATGCAT 60.250 50.000 19.57 0.00 0.00 3.96
962 1016 1.696063 GGGCGCCGGTATATATAGGA 58.304 55.000 22.54 0.00 0.00 2.94
1054 1112 1.485066 GCTAAGGTGGCAGCTAAGGTA 59.515 52.381 20.91 7.62 34.86 3.08
1055 1113 0.253327 GCTAAGGTGGCAGCTAAGGT 59.747 55.000 20.91 6.75 34.86 3.50
1091 1175 4.803426 CTCGCCGTGAGCACCTCC 62.803 72.222 0.00 0.00 44.04 4.30
1172 1259 2.093500 CACATCATTTCCGACCTCCTCA 60.093 50.000 0.00 0.00 0.00 3.86
1174 1261 2.093447 GTCACATCATTTCCGACCTCCT 60.093 50.000 0.00 0.00 0.00 3.69
1175 1262 2.280628 GTCACATCATTTCCGACCTCC 58.719 52.381 0.00 0.00 0.00 4.30
1180 1267 0.249120 AGCCGTCACATCATTTCCGA 59.751 50.000 0.00 0.00 0.00 4.55
1181 1268 0.374758 CAGCCGTCACATCATTTCCG 59.625 55.000 0.00 0.00 0.00 4.30
1184 1271 1.647545 CCGCAGCCGTCACATCATTT 61.648 55.000 0.00 0.00 0.00 2.32
1185 1272 2.108514 CCGCAGCCGTCACATCATT 61.109 57.895 0.00 0.00 0.00 2.57
1186 1273 2.512286 CCGCAGCCGTCACATCAT 60.512 61.111 0.00 0.00 0.00 2.45
1187 1274 4.758251 CCCGCAGCCGTCACATCA 62.758 66.667 0.00 0.00 0.00 3.07
1188 1275 4.760047 ACCCGCAGCCGTCACATC 62.760 66.667 0.00 0.00 0.00 3.06
1316 1406 3.790437 ATCAGCAGCCTCACCCCG 61.790 66.667 0.00 0.00 0.00 5.73
1565 1671 4.152625 GCGCTGTCGATGGTGTGC 62.153 66.667 0.00 0.00 38.10 4.57
1612 1718 2.255316 GAAGACGACTTGCTAGCTCAC 58.745 52.381 17.23 4.18 36.39 3.51
1624 1730 4.036027 TGATTACAGTATCGGGAAGACGAC 59.964 45.833 0.00 0.00 46.64 4.34
1665 1771 2.293399 TGCTTTGCTATAGCTCGATCGA 59.707 45.455 24.61 18.32 42.66 3.59
1666 1772 2.666026 TGCTTTGCTATAGCTCGATCG 58.334 47.619 24.61 9.36 42.66 3.69
1667 1773 4.493547 AGATGCTTTGCTATAGCTCGATC 58.506 43.478 24.61 16.82 42.66 3.69
1668 1774 4.533919 AGATGCTTTGCTATAGCTCGAT 57.466 40.909 24.61 9.98 42.66 3.59
1847 1960 0.742281 ACAGCACGGTCTCATGCATC 60.742 55.000 0.00 0.00 44.59 3.91
1878 1994 7.486551 TGAACGTCAATGAAACAAACTTAAAGG 59.513 33.333 0.00 0.00 0.00 3.11
1885 2001 5.227184 GTCACTGAACGTCAATGAAACAAAC 59.773 40.000 0.00 0.00 34.20 2.93
1886 2002 5.106515 TGTCACTGAACGTCAATGAAACAAA 60.107 36.000 0.00 0.00 34.20 2.83
1904 2020 2.024414 TCATGGATCGACGATGTCACT 58.976 47.619 16.49 0.00 36.38 3.41
1907 2023 1.269257 TGCTCATGGATCGACGATGTC 60.269 52.381 16.49 7.89 36.38 3.06
1954 2070 1.451207 TGTCGTGGTGTGCTTGCTT 60.451 52.632 0.00 0.00 0.00 3.91
2017 2136 4.361451 AGTAATTGTTAGCATGTGCAGC 57.639 40.909 7.83 0.00 45.16 5.25
2037 2156 0.249120 TGCCTGGATTGGTGACGTAG 59.751 55.000 0.00 0.00 0.00 3.51
2039 2158 0.606401 CTTGCCTGGATTGGTGACGT 60.606 55.000 0.00 0.00 0.00 4.34
2040 2159 0.321564 TCTTGCCTGGATTGGTGACG 60.322 55.000 0.00 0.00 0.00 4.35
2042 2161 2.905415 ATTCTTGCCTGGATTGGTGA 57.095 45.000 0.00 0.00 0.00 4.02
2053 2475 9.167311 TCTTAGAAATAACAGAGAATTCTTGCC 57.833 33.333 9.87 0.00 32.87 4.52
2081 2503 9.863845 GAATATATAGCAGTTAGAAAGACCTCC 57.136 37.037 0.00 0.00 0.00 4.30
2154 2577 2.064581 ATGGTGAGACGGGTAGGCC 61.065 63.158 0.00 0.00 0.00 5.19
2160 2583 1.165270 GGAAAACATGGTGAGACGGG 58.835 55.000 0.00 0.00 0.00 5.28
2166 2589 3.228188 AGCAGAAGGAAAACATGGTGA 57.772 42.857 0.00 0.00 0.00 4.02
2167 2590 4.096984 GGATAGCAGAAGGAAAACATGGTG 59.903 45.833 0.00 0.00 0.00 4.17
2171 2594 3.941483 CACGGATAGCAGAAGGAAAACAT 59.059 43.478 0.00 0.00 0.00 2.71
2189 2612 1.740585 TCAGTTGGAAAACACACACGG 59.259 47.619 0.00 0.00 0.00 4.94
2321 2744 2.094545 CAGCCAGGGTTTTACAGAATGC 60.095 50.000 0.00 0.00 42.53 3.56
2377 2800 3.350833 ACTGGCATGAAGTGGATTCTTC 58.649 45.455 0.00 0.00 42.67 2.87
2417 2840 0.815734 GTTCTAGCTCTGTGCCGGTA 59.184 55.000 1.90 0.00 44.23 4.02
2453 2924 2.264794 GCCACATCGGAACTCGGT 59.735 61.111 0.00 0.00 39.77 4.69
2454 2925 2.885644 CGCCACATCGGAACTCGG 60.886 66.667 0.00 0.00 39.77 4.63
2455 2926 2.158959 GTCGCCACATCGGAACTCG 61.159 63.158 0.00 0.00 36.56 4.18
2459 2930 2.434185 GCTGTCGCCACATCGGAA 60.434 61.111 0.00 0.00 36.56 4.30
2464 2935 3.321648 TCCCTGCTGTCGCCACAT 61.322 61.111 0.00 0.00 34.43 3.21
2470 2941 2.126307 CTGTCGTCCCTGCTGTCG 60.126 66.667 0.00 0.00 0.00 4.35
2509 2980 1.237954 TGGCATACAAAGCGCGGAAA 61.238 50.000 8.83 0.00 0.00 3.13
2585 3056 1.649171 GTGTACAACGTCATCTCTGCG 59.351 52.381 0.00 0.00 0.00 5.18
2678 3149 1.605738 CTGCCTTGGCCTGCTCTTT 60.606 57.895 3.32 0.00 0.00 2.52
2683 3154 2.459202 ATTTTGCTGCCTTGGCCTGC 62.459 55.000 3.32 16.01 0.00 4.85
2688 3159 3.259064 CAAGATCATTTTGCTGCCTTGG 58.741 45.455 0.00 0.00 0.00 3.61
2694 3165 5.163581 CCTCCTAACCAAGATCATTTTGCTG 60.164 44.000 0.00 0.00 0.00 4.41
2700 3171 3.137360 GCTCCCTCCTAACCAAGATCATT 59.863 47.826 0.00 0.00 0.00 2.57
2714 3185 1.546548 GGCCTATCAAATGCTCCCTCC 60.547 57.143 0.00 0.00 0.00 4.30
2717 3188 1.133668 ACTGGCCTATCAAATGCTCCC 60.134 52.381 3.32 0.00 0.00 4.30
2718 3189 2.355010 ACTGGCCTATCAAATGCTCC 57.645 50.000 3.32 0.00 0.00 4.70
2720 3191 1.753073 GCAACTGGCCTATCAAATGCT 59.247 47.619 3.32 0.00 36.11 3.79
2722 3193 3.018856 TGAGCAACTGGCCTATCAAATG 58.981 45.455 3.32 0.00 46.50 2.32
2736 3207 7.313646 TCAGTTACTCAATAGTAGTGAGCAAC 58.686 38.462 25.80 25.80 44.51 4.17
2737 3208 7.462571 TCAGTTACTCAATAGTAGTGAGCAA 57.537 36.000 23.86 16.46 45.35 3.91
2750 3221 8.725405 TCAACACTAACATTTCAGTTACTCAA 57.275 30.769 0.00 0.00 33.07 3.02
2751 3222 8.725405 TTCAACACTAACATTTCAGTTACTCA 57.275 30.769 0.00 0.00 33.07 3.41
2757 3228 8.137437 CCAGAATTTCAACACTAACATTTCAGT 58.863 33.333 0.00 0.00 0.00 3.41
2758 3229 8.352201 TCCAGAATTTCAACACTAACATTTCAG 58.648 33.333 0.00 0.00 0.00 3.02
2759 3230 8.134895 GTCCAGAATTTCAACACTAACATTTCA 58.865 33.333 0.00 0.00 0.00 2.69
2760 3231 8.352942 AGTCCAGAATTTCAACACTAACATTTC 58.647 33.333 0.00 0.00 0.00 2.17
2762 3233 7.721399 AGAGTCCAGAATTTCAACACTAACATT 59.279 33.333 0.00 0.00 0.00 2.71
2764 3235 6.483307 CAGAGTCCAGAATTTCAACACTAACA 59.517 38.462 0.00 0.00 0.00 2.41
2765 3236 6.706270 TCAGAGTCCAGAATTTCAACACTAAC 59.294 38.462 0.00 0.00 0.00 2.34
2767 3238 6.419484 TCAGAGTCCAGAATTTCAACACTA 57.581 37.500 0.00 0.00 0.00 2.74
2769 3240 6.205464 TGATTCAGAGTCCAGAATTTCAACAC 59.795 38.462 9.14 0.00 34.79 3.32
2774 3245 7.226325 CAGGTATGATTCAGAGTCCAGAATTTC 59.774 40.741 9.14 0.00 34.79 2.17
2775 3246 7.052873 CAGGTATGATTCAGAGTCCAGAATTT 58.947 38.462 9.14 4.61 34.79 1.82
2776 3247 6.157645 ACAGGTATGATTCAGAGTCCAGAATT 59.842 38.462 9.14 0.00 34.79 2.17


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

AutoCloner maintained by Alex Coulton.