Multiple sequence alignment - TraesCS4A01G048300

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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 TraesCS4A01G048300 chr4A 100.000 3509 0 0 1 3509 39054011 39050503 0.000000e+00 6481
1 TraesCS4A01G048300 chr4D 88.625 3622 197 76 8 3505 425972216 425975746 0.000000e+00 4207
2 TraesCS4A01G048300 chr4B 88.824 1879 108 33 1410 3241 522083564 522085387 0.000000e+00 2213
3 TraesCS4A01G048300 chr4B 87.405 1445 97 40 8 1414 522076911 522078308 0.000000e+00 1581
4 TraesCS4A01G048300 chr4B 89.399 283 15 6 3234 3505 522086641 522086919 3.350000e-90 342


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 TraesCS4A01G048300 chr4A 39050503 39054011 3508 True 6481.0 6481 100.0000 1 3509 1 chr4A.!!$R1 3508
1 TraesCS4A01G048300 chr4D 425972216 425975746 3530 False 4207.0 4207 88.6250 8 3505 1 chr4D.!!$F1 3497
2 TraesCS4A01G048300 chr4B 522076911 522078308 1397 False 1581.0 1581 87.4050 8 1414 1 chr4B.!!$F1 1406
3 TraesCS4A01G048300 chr4B 522083564 522086919 3355 False 1277.5 2213 89.1115 1410 3505 2 chr4B.!!$F2 2095

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
468 503 0.369589 TTATTTTTACGACGGCGGCG 59.630 50.0 36.0 36.0 43.17 6.46 F
1212 1292 0.031857 CCTGCTGTCTATCTGCTCCG 59.968 60.0 0.0 0.0 40.79 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 1363 0.530650 ACTACCAGCCGCAATCGATG 60.531 55.0 0.00 0.0 38.10 3.84 R
3087 3234 0.036577 AGCTAAGCTCTGCACAGTGG 60.037 55.0 12.44 0.0 30.62 4.00 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
81 94 2.749839 CCGCCTCGCCAAAATCCA 60.750 61.111 0.00 0.00 0.00 3.41
85 98 0.678048 GCCTCGCCAAAATCCACTCT 60.678 55.000 0.00 0.00 0.00 3.24
86 99 1.089920 CCTCGCCAAAATCCACTCTG 58.910 55.000 0.00 0.00 0.00 3.35
158 171 2.203070 AGGGATCGGTCGCAATGC 60.203 61.111 15.78 0.00 39.60 3.56
209 222 4.489737 ACCATATTCCTTCCGATCCACTA 58.510 43.478 0.00 0.00 0.00 2.74
264 285 2.657162 CGTTGTTAGTGTTGTAACGCCG 60.657 50.000 4.80 0.00 40.18 6.46
317 338 3.497932 CGGCAAGCAGAGCAGAGC 61.498 66.667 0.00 0.00 0.00 4.09
334 358 1.807142 GAGCAGAACCAGGTGTAAAGC 59.193 52.381 0.00 0.00 0.00 3.51
342 366 0.517316 CAGGTGTAAAGCGGCAGTTC 59.483 55.000 1.45 0.00 0.00 3.01
343 367 0.605589 AGGTGTAAAGCGGCAGTTCC 60.606 55.000 1.45 0.00 0.00 3.62
344 368 1.583495 GGTGTAAAGCGGCAGTTCCC 61.583 60.000 1.45 0.00 0.00 3.97
345 369 1.302993 TGTAAAGCGGCAGTTCCCC 60.303 57.895 1.45 0.00 0.00 4.81
346 370 2.044555 GTAAAGCGGCAGTTCCCCC 61.045 63.158 1.45 0.00 0.00 5.40
367 391 2.196595 CCTCCCACTATCCAAAGACCA 58.803 52.381 0.00 0.00 0.00 4.02
368 392 2.092914 CCTCCCACTATCCAAAGACCAC 60.093 54.545 0.00 0.00 0.00 4.16
369 393 1.913419 TCCCACTATCCAAAGACCACC 59.087 52.381 0.00 0.00 0.00 4.61
376 400 5.066505 CACTATCCAAAGACCACCTTAATGC 59.933 44.000 0.00 0.00 34.00 3.56
410 434 2.501008 CGCCTTAAACGCCGTTGC 60.501 61.111 1.95 1.04 0.00 4.17
411 435 2.951458 GCCTTAAACGCCGTTGCT 59.049 55.556 1.95 0.00 34.43 3.91
412 436 1.442017 GCCTTAAACGCCGTTGCTG 60.442 57.895 1.95 0.00 34.43 4.41
468 503 0.369589 TTATTTTTACGACGGCGGCG 59.630 50.000 36.00 36.00 43.17 6.46
469 504 1.419874 TATTTTTACGACGGCGGCGG 61.420 55.000 39.66 21.27 43.17 6.13
539 574 1.544759 GGTTGGGCCTCTTCTTTTCGA 60.545 52.381 4.53 0.00 0.00 3.71
543 581 1.443802 GGCCTCTTCTTTTCGACTGG 58.556 55.000 0.00 0.00 0.00 4.00
556 594 1.067669 TCGACTGGCAGTCATATGCTC 59.932 52.381 38.18 16.68 45.30 4.26
622 660 5.895216 CATGTCTGCAGTTTTTCTTTTCC 57.105 39.130 14.67 0.00 0.00 3.13
623 661 5.594926 CATGTCTGCAGTTTTTCTTTTCCT 58.405 37.500 14.67 0.00 0.00 3.36
624 662 4.997565 TGTCTGCAGTTTTTCTTTTCCTG 58.002 39.130 14.67 0.00 0.00 3.86
625 663 4.142182 TGTCTGCAGTTTTTCTTTTCCTGG 60.142 41.667 14.67 0.00 0.00 4.45
626 664 4.023291 TCTGCAGTTTTTCTTTTCCTGGT 58.977 39.130 14.67 0.00 0.00 4.00
627 665 4.466015 TCTGCAGTTTTTCTTTTCCTGGTT 59.534 37.500 14.67 0.00 0.00 3.67
628 666 5.046663 TCTGCAGTTTTTCTTTTCCTGGTTT 60.047 36.000 14.67 0.00 0.00 3.27
629 667 6.153680 TCTGCAGTTTTTCTTTTCCTGGTTTA 59.846 34.615 14.67 0.00 0.00 2.01
631 669 6.760770 TGCAGTTTTTCTTTTCCTGGTTTATG 59.239 34.615 0.00 0.00 0.00 1.90
682 727 7.592736 AGTTATTATTTTAGCTTTAGGCCCCT 58.407 34.615 0.00 0.00 43.05 4.79
683 728 8.729997 AGTTATTATTTTAGCTTTAGGCCCCTA 58.270 33.333 0.00 0.00 43.05 3.53
883 928 2.666317 CTTTCTCCTCTCCTCTCCTCC 58.334 57.143 0.00 0.00 0.00 4.30
926 972 2.178521 GTCGTCGACATGACCGCT 59.821 61.111 20.28 0.00 45.23 5.52
929 975 2.152699 CGTCGACATGACCGCTGAC 61.153 63.158 17.16 0.00 45.23 3.51
972 1018 1.211457 AGTGAGTCGTAGGGATACGGT 59.789 52.381 7.84 0.00 43.07 4.83
973 1019 2.435805 AGTGAGTCGTAGGGATACGGTA 59.564 50.000 7.84 0.00 43.07 4.02
974 1020 3.072184 AGTGAGTCGTAGGGATACGGTAT 59.928 47.826 0.00 0.00 43.07 2.73
975 1021 4.284490 AGTGAGTCGTAGGGATACGGTATA 59.716 45.833 0.00 0.00 43.07 1.47
976 1022 4.390297 GTGAGTCGTAGGGATACGGTATAC 59.610 50.000 1.49 1.49 43.07 1.47
992 1046 3.303659 GGTATACGGTTACAGTCGAGCTC 60.304 52.174 2.73 2.73 0.00 4.09
1200 1254 1.302832 GCTGGTAAGTGCCTGCTGT 60.303 57.895 9.53 0.00 46.00 4.40
1203 1283 1.550524 CTGGTAAGTGCCTGCTGTCTA 59.449 52.381 0.00 0.00 0.00 2.59
1205 1285 2.168521 TGGTAAGTGCCTGCTGTCTATC 59.831 50.000 0.00 0.00 0.00 2.08
1207 1287 2.687700 AAGTGCCTGCTGTCTATCTG 57.312 50.000 0.00 0.00 0.00 2.90
1209 1289 0.177604 GTGCCTGCTGTCTATCTGCT 59.822 55.000 0.00 0.00 40.79 4.24
1212 1292 0.031857 CCTGCTGTCTATCTGCTCCG 59.968 60.000 0.00 0.00 40.79 4.63
1223 1303 4.648626 TGCTCCGGCTTGCTGCTT 62.649 61.111 13.41 0.00 42.39 3.91
1224 1304 4.112341 GCTCCGGCTTGCTGCTTG 62.112 66.667 0.00 0.00 42.39 4.01
1225 1305 3.437795 CTCCGGCTTGCTGCTTGG 61.438 66.667 0.00 5.36 42.39 3.61
1228 1308 4.047059 CGGCTTGCTGCTTGGGTG 62.047 66.667 0.00 0.00 42.39 4.61
1229 1309 4.368543 GGCTTGCTGCTTGGGTGC 62.369 66.667 0.00 0.00 42.39 5.01
1230 1310 3.608662 GCTTGCTGCTTGGGTGCA 61.609 61.111 0.00 0.00 41.05 4.57
1231 1311 2.337532 CTTGCTGCTTGGGTGCAC 59.662 61.111 8.80 8.80 38.12 4.57
1232 1312 2.441717 TTGCTGCTTGGGTGCACA 60.442 55.556 20.43 0.00 38.12 4.57
1233 1313 2.416244 CTTGCTGCTTGGGTGCACAG 62.416 60.000 20.43 8.83 38.12 3.66
1234 1314 2.908940 GCTGCTTGGGTGCACAGT 60.909 61.111 20.43 0.00 38.12 3.55
1235 1315 2.492773 GCTGCTTGGGTGCACAGTT 61.493 57.895 20.43 0.00 38.12 3.16
1239 1319 0.310854 GCTTGGGTGCACAGTTACAC 59.689 55.000 20.43 0.00 36.03 2.90
1257 1337 3.620300 CTTACACGTCGCGAGGGCA 62.620 63.158 29.83 13.41 39.92 5.36
1289 1373 1.600957 AGCTGATTTCCATCGATTGCG 59.399 47.619 0.00 0.00 39.35 4.85
1355 1439 0.456628 GGAAGGTAGCTGAGACGTCC 59.543 60.000 13.01 4.42 0.00 4.79
1552 1636 2.987547 TCCCCGTCCGTGACACTC 60.988 66.667 3.68 0.00 32.09 3.51
1553 1637 3.299977 CCCCGTCCGTGACACTCA 61.300 66.667 3.68 0.00 32.09 3.41
1554 1638 2.646175 CCCCGTCCGTGACACTCAT 61.646 63.158 3.68 0.00 32.09 2.90
1555 1639 1.446099 CCCGTCCGTGACACTCATG 60.446 63.158 3.68 0.00 33.30 3.07
1556 1640 1.584495 CCGTCCGTGACACTCATGA 59.416 57.895 3.68 0.00 35.46 3.07
1557 1641 0.456824 CCGTCCGTGACACTCATGAG 60.457 60.000 21.37 21.37 35.46 2.90
1558 1642 1.073216 CGTCCGTGACACTCATGAGC 61.073 60.000 22.83 7.24 35.46 4.26
1559 1643 1.073216 GTCCGTGACACTCATGAGCG 61.073 60.000 22.83 16.00 35.46 5.03
1560 1644 2.447887 CCGTGACACTCATGAGCGC 61.448 63.158 22.83 11.87 35.46 5.92
1561 1645 2.447887 CGTGACACTCATGAGCGCC 61.448 63.158 22.83 6.35 35.46 6.53
1562 1646 2.103042 GTGACACTCATGAGCGCCC 61.103 63.158 22.83 9.38 0.00 6.13
1563 1647 2.887568 GACACTCATGAGCGCCCG 60.888 66.667 22.83 8.64 0.00 6.13
1616 1700 1.195900 GTGTGCGTGGCGAAGAATTAA 59.804 47.619 0.00 0.00 0.00 1.40
1617 1701 1.874231 TGTGCGTGGCGAAGAATTAAA 59.126 42.857 0.00 0.00 0.00 1.52
1743 1827 3.192922 GCGTACATGGCCACGGAC 61.193 66.667 8.16 5.52 38.57 4.79
2012 2096 3.534160 CGTGGACGACGGTTTCAG 58.466 61.111 1.57 0.00 44.85 3.02
2505 2589 2.650116 CGTGGACCCCAGAGAGGTG 61.650 68.421 0.00 0.00 37.88 4.00
2594 2678 6.129874 AGATAGGAAGGTTTTGGATTTAGCC 58.870 40.000 0.00 0.00 0.00 3.93
2597 2681 3.366985 GGAAGGTTTTGGATTTAGCCGTG 60.367 47.826 0.00 0.00 0.00 4.94
2620 2710 5.104900 TGGAGATTTTGTAGGAGCCTAGTTC 60.105 44.000 0.00 0.00 0.00 3.01
2636 2726 5.008316 GCCTAGTTCGTTTTCCTTTTTCTGA 59.992 40.000 0.00 0.00 0.00 3.27
2646 2736 7.413644 GTTTTCCTTTTTCTGACAGAGAAGAG 58.586 38.462 22.49 15.74 41.86 2.85
2657 2747 7.206687 TCTGACAGAGAAGAGAAGAAAAGAAC 58.793 38.462 0.00 0.00 0.00 3.01
2662 2758 7.070074 ACAGAGAAGAGAAGAAAAGAACTGGTA 59.930 37.037 0.00 0.00 0.00 3.25
2687 2783 0.395686 CTGTGAGCCGATGGATCCAT 59.604 55.000 27.66 27.66 37.30 3.41
2688 2784 1.620323 CTGTGAGCCGATGGATCCATA 59.380 52.381 27.38 7.92 37.30 2.74
2689 2785 1.344438 TGTGAGCCGATGGATCCATAC 59.656 52.381 27.38 19.71 37.30 2.39
2692 2791 0.979665 AGCCGATGGATCCATACCAG 59.020 55.000 27.38 17.35 40.89 4.00
2694 2793 0.036010 CCGATGGATCCATACCAGCC 60.036 60.000 27.38 12.57 40.20 4.85
2697 2796 2.719739 GATGGATCCATACCAGCCATG 58.280 52.381 27.38 0.00 39.32 3.66
2707 2806 3.723172 CAGCCATGGAATCGACGG 58.277 61.111 18.40 0.00 0.00 4.79
2799 2905 4.693283 TGCAGTTACTACCAGATGTATGC 58.307 43.478 0.00 0.00 0.00 3.14
2800 2906 4.161377 TGCAGTTACTACCAGATGTATGCA 59.839 41.667 0.00 0.00 34.40 3.96
2801 2907 5.163311 TGCAGTTACTACCAGATGTATGCAT 60.163 40.000 3.79 3.79 32.90 3.96
2802 2908 5.178252 GCAGTTACTACCAGATGTATGCATG 59.822 44.000 10.16 0.00 35.07 4.06
2803 2909 6.283694 CAGTTACTACCAGATGTATGCATGT 58.716 40.000 10.16 0.00 35.07 3.21
2804 2910 6.201615 CAGTTACTACCAGATGTATGCATGTG 59.798 42.308 10.16 13.12 43.54 3.21
2805 2911 4.760530 ACTACCAGATGTATGCATGTGT 57.239 40.909 17.56 9.68 42.71 3.72
2806 2912 4.697514 ACTACCAGATGTATGCATGTGTC 58.302 43.478 17.56 4.23 42.71 3.67
2807 2913 3.632643 ACCAGATGTATGCATGTGTCA 57.367 42.857 17.56 3.91 42.71 3.58
2812 2918 5.270853 CAGATGTATGCATGTGTCAATGTG 58.729 41.667 10.16 0.00 40.32 3.21
2825 2931 4.092529 GTGTCAATGTGTGTCTAGATGCTG 59.907 45.833 0.00 0.00 0.00 4.41
2836 2942 1.976132 TAGATGCTGCTCACCCTGGC 61.976 60.000 0.00 0.00 0.00 4.85
2837 2948 4.790962 ATGCTGCTCACCCTGGCG 62.791 66.667 0.00 0.00 0.00 5.69
2867 2978 2.875933 TGTTTTTCGTCCCTGTAAGCAG 59.124 45.455 0.00 0.00 42.22 4.24
2937 3070 3.305403 CGGCATATCGAGTAATCAGTGGT 60.305 47.826 0.00 0.00 0.00 4.16
2938 3071 3.990469 GGCATATCGAGTAATCAGTGGTG 59.010 47.826 0.00 0.00 0.00 4.17
2939 3072 3.990469 GCATATCGAGTAATCAGTGGTGG 59.010 47.826 0.00 0.00 0.00 4.61
2940 3073 2.604046 ATCGAGTAATCAGTGGTGGC 57.396 50.000 0.00 0.00 0.00 5.01
2941 3074 1.262417 TCGAGTAATCAGTGGTGGCA 58.738 50.000 0.00 0.00 0.00 4.92
2943 3076 2.159099 TCGAGTAATCAGTGGTGGCATC 60.159 50.000 0.00 0.00 0.00 3.91
2946 3079 2.511218 AGTAATCAGTGGTGGCATCCAT 59.489 45.455 11.13 0.00 39.81 3.41
2948 3081 0.184451 ATCAGTGGTGGCATCCATCC 59.816 55.000 11.13 0.00 39.81 3.51
2949 3082 1.206811 TCAGTGGTGGCATCCATCCA 61.207 55.000 11.13 1.08 39.81 3.41
2950 3083 0.106369 CAGTGGTGGCATCCATCCAT 60.106 55.000 11.13 0.00 39.81 3.41
2985 3118 0.821517 CACCGCCACTGTGGAGTATA 59.178 55.000 30.23 0.00 45.51 1.47
3063 3210 0.683828 ATTGATGGTGGCGGATGCAA 60.684 50.000 0.00 0.00 45.35 4.08
3096 3243 4.624364 CTGACGCCCCACTGTGCA 62.624 66.667 1.29 0.00 0.00 4.57
3097 3244 4.624364 TGACGCCCCACTGTGCAG 62.624 66.667 1.29 0.00 0.00 4.41
3115 3262 2.572664 GAGCTTAGCTTCGCTCGTC 58.427 57.895 17.60 1.36 42.62 4.20
3153 3300 0.361184 GATCGTTCGGTCGTTCGTTG 59.639 55.000 0.00 0.00 0.00 4.10
3156 3303 1.481819 CGTTCGGTCGTTCGTTGGTT 61.482 55.000 0.92 0.00 0.00 3.67
3166 3313 0.658897 TTCGTTGGTTCGTTTGGCTC 59.341 50.000 0.00 0.00 0.00 4.70
3195 3358 1.602377 GGGAATATTGCACTGTACGCC 59.398 52.381 9.34 0.00 0.00 5.68
3265 4689 1.221414 GTAGGTGCGAGATGAATGCC 58.779 55.000 0.00 0.00 0.00 4.40
3271 4695 0.882042 GCGAGATGAATGCCGTCCAT 60.882 55.000 0.00 0.00 35.06 3.41
3302 4726 3.081133 CTCCGGTGTCGCGAAATG 58.919 61.111 12.06 1.80 34.56 2.32
3315 4739 1.471501 GCGAAATGGGAAAAGGCCATC 60.472 52.381 5.01 0.00 0.00 3.51
3316 4740 1.136891 CGAAATGGGAAAAGGCCATCC 59.863 52.381 5.01 9.80 34.85 3.51
3320 4744 0.032217 TGGGAAAAGGCCATCCATCC 60.032 55.000 20.07 12.81 37.46 3.51
3321 4745 0.032217 GGGAAAAGGCCATCCATCCA 60.032 55.000 20.07 0.00 37.46 3.41
3322 4746 1.413517 GGGAAAAGGCCATCCATCCAT 60.414 52.381 20.07 0.00 37.46 3.41
3323 4747 1.966354 GGAAAAGGCCATCCATCCATC 59.034 52.381 15.27 0.00 35.71 3.51
3326 4750 1.998444 AAGGCCATCCATCCATCGCA 61.998 55.000 5.01 0.00 33.74 5.10
3327 4751 2.263741 GGCCATCCATCCATCGCAC 61.264 63.158 0.00 0.00 0.00 5.34
3406 4834 0.385098 GGTTTTGTCGCCGTGTAAGC 60.385 55.000 0.00 0.00 0.00 3.09
3436 4864 3.495124 CCTTTGGGATGTGCGTTTG 57.505 52.632 0.00 0.00 33.58 2.93
3441 4869 2.500509 TGGGATGTGCGTTTGTTTTC 57.499 45.000 0.00 0.00 0.00 2.29
3442 4870 2.028130 TGGGATGTGCGTTTGTTTTCT 58.972 42.857 0.00 0.00 0.00 2.52
3482 4929 2.808543 GTGGTGTCACTTCATCAACTCC 59.191 50.000 2.35 0.00 40.58 3.85
3505 4952 2.901192 TCAGGGGACGTAAAAGTGATGA 59.099 45.455 0.00 0.00 0.00 2.92
3506 4953 3.517901 TCAGGGGACGTAAAAGTGATGAT 59.482 43.478 0.00 0.00 0.00 2.45
3507 4954 3.623060 CAGGGGACGTAAAAGTGATGATG 59.377 47.826 0.00 0.00 0.00 3.07
3508 4955 2.354821 GGGGACGTAAAAGTGATGATGC 59.645 50.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.351465 TGTTTTATCGATTCTCTTCTGTGCC 59.649 40.000 1.71 0.00 0.00 5.01
1 2 6.408858 TGTTTTATCGATTCTCTTCTGTGC 57.591 37.500 1.71 0.00 0.00 4.57
2 3 7.959651 CCTTTGTTTTATCGATTCTCTTCTGTG 59.040 37.037 1.71 0.00 0.00 3.66
3 4 7.878127 TCCTTTGTTTTATCGATTCTCTTCTGT 59.122 33.333 1.71 0.00 0.00 3.41
4 5 8.256611 TCCTTTGTTTTATCGATTCTCTTCTG 57.743 34.615 1.71 0.00 0.00 3.02
5 6 8.887717 CATCCTTTGTTTTATCGATTCTCTTCT 58.112 33.333 1.71 0.00 0.00 2.85
6 7 8.883731 TCATCCTTTGTTTTATCGATTCTCTTC 58.116 33.333 1.71 0.00 0.00 2.87
81 94 1.134560 GTTATCCGGCGAAGTCAGAGT 59.865 52.381 9.30 0.00 0.00 3.24
85 98 0.899720 AAGGTTATCCGGCGAAGTCA 59.100 50.000 9.30 0.00 39.05 3.41
86 99 2.862536 GTTAAGGTTATCCGGCGAAGTC 59.137 50.000 9.30 0.00 39.05 3.01
139 152 1.595382 CATTGCGACCGATCCCTCC 60.595 63.158 0.00 0.00 0.00 4.30
143 156 2.537560 CCAGCATTGCGACCGATCC 61.538 63.158 2.38 0.00 0.00 3.36
144 157 3.017323 CCAGCATTGCGACCGATC 58.983 61.111 2.38 0.00 0.00 3.69
169 182 2.559668 TGGTTTTCTGAGTCGGTCGTAT 59.440 45.455 0.00 0.00 0.00 3.06
302 323 0.954449 TTCTGCTCTGCTCTGCTTGC 60.954 55.000 0.00 0.00 0.00 4.01
303 324 0.797542 GTTCTGCTCTGCTCTGCTTG 59.202 55.000 0.00 0.00 0.00 4.01
305 326 1.296068 GGTTCTGCTCTGCTCTGCT 59.704 57.895 0.00 0.00 0.00 4.24
306 327 1.004080 TGGTTCTGCTCTGCTCTGC 60.004 57.895 0.00 0.00 0.00 4.26
314 335 1.807142 GCTTTACACCTGGTTCTGCTC 59.193 52.381 0.00 0.00 0.00 4.26
315 336 1.878102 CGCTTTACACCTGGTTCTGCT 60.878 52.381 0.00 0.00 0.00 4.24
316 337 0.517316 CGCTTTACACCTGGTTCTGC 59.483 55.000 0.00 0.00 0.00 4.26
317 338 1.156736 CCGCTTTACACCTGGTTCTG 58.843 55.000 0.00 0.00 0.00 3.02
344 368 0.846693 CTTTGGATAGTGGGAGGGGG 59.153 60.000 0.00 0.00 0.00 5.40
345 369 1.490910 GTCTTTGGATAGTGGGAGGGG 59.509 57.143 0.00 0.00 0.00 4.79
346 370 1.490910 GGTCTTTGGATAGTGGGAGGG 59.509 57.143 0.00 0.00 0.00 4.30
349 373 1.913419 GGTGGTCTTTGGATAGTGGGA 59.087 52.381 0.00 0.00 0.00 4.37
367 391 6.183360 CCGTGAAATTAAGATGGCATTAAGGT 60.183 38.462 0.00 0.00 0.00 3.50
368 392 6.208644 CCGTGAAATTAAGATGGCATTAAGG 58.791 40.000 0.00 0.00 0.00 2.69
369 393 5.687285 GCCGTGAAATTAAGATGGCATTAAG 59.313 40.000 0.00 0.00 40.86 1.85
376 400 1.268539 GGCGCCGTGAAATTAAGATGG 60.269 52.381 12.58 0.00 0.00 3.51
407 431 2.282603 GGGGGTTTACGGCAGCAA 60.283 61.111 0.00 0.00 0.00 3.91
410 434 0.322997 TGATTGGGGGTTTACGGCAG 60.323 55.000 0.00 0.00 0.00 4.85
411 435 0.333312 ATGATTGGGGGTTTACGGCA 59.667 50.000 0.00 0.00 0.00 5.69
412 436 0.744281 CATGATTGGGGGTTTACGGC 59.256 55.000 0.00 0.00 0.00 5.68
512 547 4.011517 GAGGCCCAACCCGAACGA 62.012 66.667 0.00 0.00 40.58 3.85
522 557 1.056660 AGTCGAAAAGAAGAGGCCCA 58.943 50.000 0.00 0.00 0.00 5.36
539 574 1.504912 AGGAGCATATGACTGCCAGT 58.495 50.000 6.97 0.00 43.33 4.00
621 659 1.202580 CGCTCCTCCTCATAAACCAGG 60.203 57.143 0.00 0.00 0.00 4.45
622 660 1.757118 TCGCTCCTCCTCATAAACCAG 59.243 52.381 0.00 0.00 0.00 4.00
623 661 1.860641 TCGCTCCTCCTCATAAACCA 58.139 50.000 0.00 0.00 0.00 3.67
624 662 2.365617 TGATCGCTCCTCCTCATAAACC 59.634 50.000 0.00 0.00 0.00 3.27
625 663 3.648009 CTGATCGCTCCTCCTCATAAAC 58.352 50.000 0.00 0.00 0.00 2.01
626 664 2.036475 GCTGATCGCTCCTCCTCATAAA 59.964 50.000 2.84 0.00 35.14 1.40
627 665 1.615883 GCTGATCGCTCCTCCTCATAA 59.384 52.381 2.84 0.00 35.14 1.90
628 666 1.252175 GCTGATCGCTCCTCCTCATA 58.748 55.000 2.84 0.00 35.14 2.15
629 667 1.804396 CGCTGATCGCTCCTCCTCAT 61.804 60.000 7.71 0.00 36.13 2.90
631 669 2.334653 CGCTGATCGCTCCTCCTC 59.665 66.667 7.71 0.00 36.13 3.71
726 771 6.911308 TCTCTAAAAATTCCTATCCCTTGGG 58.089 40.000 0.00 0.00 0.00 4.12
909 955 2.152699 CAGCGGTCATGTCGACGAC 61.153 63.158 20.97 20.97 46.42 4.34
926 972 4.329545 GCCAGCTTCACCCGGTCA 62.330 66.667 0.00 0.00 0.00 4.02
946 992 0.663688 CCCTACGACTCACTCATCCG 59.336 60.000 0.00 0.00 0.00 4.18
972 1018 2.541346 CGAGCTCGACTGTAACCGTATA 59.459 50.000 32.06 0.00 43.02 1.47
973 1019 1.329906 CGAGCTCGACTGTAACCGTAT 59.670 52.381 32.06 0.00 43.02 3.06
974 1020 0.723414 CGAGCTCGACTGTAACCGTA 59.277 55.000 32.06 0.00 43.02 4.02
975 1021 0.952497 TCGAGCTCGACTGTAACCGT 60.952 55.000 33.84 0.00 44.22 4.83
976 1022 0.247735 CTCGAGCTCGACTGTAACCG 60.248 60.000 33.84 18.03 44.22 4.44
977 1023 0.523757 GCTCGAGCTCGACTGTAACC 60.524 60.000 33.84 12.47 44.22 2.85
978 1024 0.858135 CGCTCGAGCTCGACTGTAAC 60.858 60.000 33.84 17.15 44.22 2.50
979 1025 1.424240 CGCTCGAGCTCGACTGTAA 59.576 57.895 33.84 13.66 44.22 2.41
992 1046 2.890109 GCATCTTCCATGGCGCTCG 61.890 63.158 6.96 0.00 0.00 5.03
1011 1065 3.691297 TACCCTCGGCTTCCCCTCC 62.691 68.421 0.00 0.00 0.00 4.30
1023 1077 1.718280 ACTCCCGGATGATTACCCTC 58.282 55.000 0.73 0.00 0.00 4.30
1173 1227 3.134458 GGCACTTACCAGCATGAGATAC 58.866 50.000 0.00 0.00 39.69 2.24
1176 1230 1.065926 CAGGCACTTACCAGCATGAGA 60.066 52.381 0.00 0.00 44.53 3.27
1200 1254 1.045350 AGCAAGCCGGAGCAGATAGA 61.045 55.000 5.05 0.00 43.56 1.98
1203 1283 2.124819 CAGCAAGCCGGAGCAGAT 60.125 61.111 5.05 0.00 43.56 2.90
1233 1313 1.640915 CTCGCGACGTGTAAGTGTAAC 59.359 52.381 3.71 0.00 0.00 2.50
1234 1314 1.400113 CCTCGCGACGTGTAAGTGTAA 60.400 52.381 3.71 0.00 0.00 2.41
1235 1315 0.166597 CCTCGCGACGTGTAAGTGTA 59.833 55.000 3.71 0.00 0.00 2.90
1239 1319 2.879462 GCCCTCGCGACGTGTAAG 60.879 66.667 3.71 0.00 0.00 2.34
1279 1363 0.530650 ACTACCAGCCGCAATCGATG 60.531 55.000 0.00 0.00 38.10 3.84
1289 1373 0.539669 AAAGCAACCCACTACCAGCC 60.540 55.000 0.00 0.00 0.00 4.85
1568 1652 2.852495 AATGCCACAGCGTACTCGGG 62.852 60.000 0.00 0.00 44.31 5.14
1569 1653 1.447838 AATGCCACAGCGTACTCGG 60.448 57.895 0.00 0.00 44.31 4.63
1570 1654 0.735978 TCAATGCCACAGCGTACTCG 60.736 55.000 0.00 0.00 44.31 4.18
1571 1655 1.656652 ATCAATGCCACAGCGTACTC 58.343 50.000 0.00 0.00 44.31 2.59
1572 1656 2.009774 GAATCAATGCCACAGCGTACT 58.990 47.619 0.00 0.00 44.31 2.73
1573 1657 1.267532 CGAATCAATGCCACAGCGTAC 60.268 52.381 0.00 0.00 44.31 3.67
1574 1658 1.006086 CGAATCAATGCCACAGCGTA 58.994 50.000 0.00 0.00 44.31 4.42
1575 1659 1.647545 CCGAATCAATGCCACAGCGT 61.648 55.000 0.00 0.00 44.31 5.07
1576 1660 1.063006 CCGAATCAATGCCACAGCG 59.937 57.895 0.00 0.00 44.31 5.18
1577 1661 1.226773 GCCGAATCAATGCCACAGC 60.227 57.895 0.00 0.00 40.48 4.40
1616 1700 2.158841 CGCGGCGCCATTAATTAGTATT 59.841 45.455 28.98 0.00 0.00 1.89
1617 1701 1.730064 CGCGGCGCCATTAATTAGTAT 59.270 47.619 28.98 0.00 0.00 2.12
1743 1827 1.006102 AGACGCCTCGTTGGACTTG 60.006 57.895 1.63 0.00 41.37 3.16
2505 2589 1.446099 TCGCTGCCGAGTCAATCAC 60.446 57.895 0.00 0.00 38.82 3.06
2532 2616 0.749818 TAGCTCTCTCTGGCTGGTCG 60.750 60.000 0.00 0.00 39.31 4.79
2594 2678 2.093447 AGGCTCCTACAAAATCTCCACG 60.093 50.000 0.00 0.00 0.00 4.94
2597 2681 5.360649 AACTAGGCTCCTACAAAATCTCC 57.639 43.478 0.00 0.00 0.00 3.71
2620 2710 5.734855 TCTCTGTCAGAAAAAGGAAAACG 57.265 39.130 3.67 0.00 0.00 3.60
2636 2726 6.126911 ACCAGTTCTTTTCTTCTCTTCTCTGT 60.127 38.462 0.00 0.00 0.00 3.41
2646 2736 2.742589 CCGCCTACCAGTTCTTTTCTTC 59.257 50.000 0.00 0.00 0.00 2.87
2657 2747 2.185350 CTCACAGCCGCCTACCAG 59.815 66.667 0.00 0.00 0.00 4.00
2687 2783 0.104120 CGTCGATTCCATGGCTGGTA 59.896 55.000 6.96 0.00 43.61 3.25
2688 2784 1.153369 CGTCGATTCCATGGCTGGT 60.153 57.895 6.96 0.00 43.61 4.00
2689 2785 1.889105 CCGTCGATTCCATGGCTGG 60.889 63.158 6.96 0.00 44.64 4.85
2692 2791 1.887707 GTCCCGTCGATTCCATGGC 60.888 63.158 6.96 0.00 0.00 4.40
2694 2793 0.459899 TCTGTCCCGTCGATTCCATG 59.540 55.000 0.00 0.00 0.00 3.66
2697 2796 2.000447 CTTTTCTGTCCCGTCGATTCC 59.000 52.381 0.00 0.00 0.00 3.01
2707 2806 2.926838 GTCGCATCTCTCTTTTCTGTCC 59.073 50.000 0.00 0.00 0.00 4.02
2799 2905 5.446875 GCATCTAGACACACATTGACACATG 60.447 44.000 0.00 0.00 0.00 3.21
2800 2906 4.633126 GCATCTAGACACACATTGACACAT 59.367 41.667 0.00 0.00 0.00 3.21
2801 2907 3.996363 GCATCTAGACACACATTGACACA 59.004 43.478 0.00 0.00 0.00 3.72
2802 2908 4.092529 CAGCATCTAGACACACATTGACAC 59.907 45.833 0.00 0.00 0.00 3.67
2803 2909 4.248058 CAGCATCTAGACACACATTGACA 58.752 43.478 0.00 0.00 0.00 3.58
2804 2910 3.063180 GCAGCATCTAGACACACATTGAC 59.937 47.826 0.00 0.00 0.00 3.18
2805 2911 3.055602 AGCAGCATCTAGACACACATTGA 60.056 43.478 0.00 0.00 0.00 2.57
2806 2912 3.268330 AGCAGCATCTAGACACACATTG 58.732 45.455 0.00 0.00 0.00 2.82
2807 2913 3.055602 TGAGCAGCATCTAGACACACATT 60.056 43.478 0.00 0.00 0.00 2.71
2812 2918 1.472376 GGGTGAGCAGCATCTAGACAC 60.472 57.143 0.00 0.00 0.00 3.67
2825 2931 4.828925 GAGAGCGCCAGGGTGAGC 62.829 72.222 2.29 0.00 0.00 4.26
2836 2942 0.602905 ACGAAAAACAGGGGAGAGCG 60.603 55.000 0.00 0.00 0.00 5.03
2837 2948 1.157585 GACGAAAAACAGGGGAGAGC 58.842 55.000 0.00 0.00 0.00 4.09
2838 2949 1.610886 GGGACGAAAAACAGGGGAGAG 60.611 57.143 0.00 0.00 0.00 3.20
2924 3057 2.092968 TGGATGCCACCACTGATTACTC 60.093 50.000 0.00 0.00 34.77 2.59
2937 3070 0.406750 GGATGGATGGATGGATGCCA 59.593 55.000 0.00 0.00 40.24 4.92
2938 3071 0.406750 TGGATGGATGGATGGATGCC 59.593 55.000 0.00 0.00 0.00 4.40
2939 3072 1.891150 GTTGGATGGATGGATGGATGC 59.109 52.381 0.00 0.00 0.00 3.91
2940 3073 3.181437 TGAGTTGGATGGATGGATGGATG 60.181 47.826 0.00 0.00 0.00 3.51
2941 3074 3.058341 TGAGTTGGATGGATGGATGGAT 58.942 45.455 0.00 0.00 0.00 3.41
2943 3076 3.301794 TTGAGTTGGATGGATGGATGG 57.698 47.619 0.00 0.00 0.00 3.51
2946 3079 2.025131 TGCATTGAGTTGGATGGATGGA 60.025 45.455 0.00 0.00 0.00 3.41
2948 3081 2.100252 GGTGCATTGAGTTGGATGGATG 59.900 50.000 0.00 0.00 0.00 3.51
2949 3082 2.381911 GGTGCATTGAGTTGGATGGAT 58.618 47.619 0.00 0.00 0.00 3.41
2950 3083 1.838112 GGTGCATTGAGTTGGATGGA 58.162 50.000 0.00 0.00 0.00 3.41
3021 3168 3.474034 GTCGAGCTCGCACAGTGC 61.474 66.667 30.97 16.21 40.69 4.40
3087 3234 0.036577 AGCTAAGCTCTGCACAGTGG 60.037 55.000 12.44 0.00 30.62 4.00
3139 3286 1.208009 CGAACCAACGAACGACCGAA 61.208 55.000 8.04 0.00 35.09 4.30
3140 3287 1.658102 CGAACCAACGAACGACCGA 60.658 57.895 8.04 0.00 35.09 4.69
3142 3289 0.652071 AAACGAACCAACGAACGACC 59.348 50.000 0.14 0.00 37.03 4.79
3143 3290 1.592830 CCAAACGAACCAACGAACGAC 60.593 52.381 0.14 0.00 37.03 4.34
3153 3300 1.777199 CGTACGAGCCAAACGAACC 59.223 57.895 10.44 0.00 38.89 3.62
3166 3313 1.562575 GCAATATTCCCGGGCGTACG 61.563 60.000 18.49 11.84 0.00 3.67
3231 3394 0.383231 CCTACGCTACGTTAGGTGGG 59.617 60.000 0.00 0.00 41.54 4.61
3265 4689 1.875576 GCTCCATGCCTCTTATGGACG 60.876 57.143 2.73 2.06 46.84 4.79
3271 4695 1.402896 CCGGAGCTCCATGCCTCTTA 61.403 60.000 31.67 0.00 44.23 2.10
3302 4726 0.032217 TGGATGGATGGCCTTTTCCC 60.032 55.000 3.32 0.00 34.31 3.97
3406 4834 2.118132 CCAAAGGGCGAATGGGATG 58.882 57.895 0.00 0.00 0.00 3.51
3426 4854 1.476074 CGCAGAAAACAAACGCACAT 58.524 45.000 0.00 0.00 0.00 3.21
3432 4860 5.574815 ATGTAAATGCGCAGAAAACAAAC 57.425 34.783 18.32 5.89 0.00 2.93
3436 4864 6.138546 CGTACATATGTAAATGCGCAGAAAAC 59.861 38.462 18.32 11.90 31.52 2.43
3441 4869 4.445351 CACGTACATATGTAAATGCGCAG 58.555 43.478 18.32 9.03 31.52 5.18
3442 4870 3.246463 CCACGTACATATGTAAATGCGCA 59.754 43.478 14.96 14.96 31.52 6.09
3482 4929 3.328382 TCACTTTTACGTCCCCTGATG 57.672 47.619 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.