Multiple sequence alignment - TraesCS3B01G610900

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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 TraesCS3B01G610900 chr3B 100.000 3048 0 0 1 3048 829113036 829116083 0.000000e+00 5629.0
1 TraesCS3B01G610900 chr3D 89.025 2041 105 34 1 1967 611407363 611409358 0.000000e+00 2418.0
2 TraesCS3B01G610900 chr3D 96.075 535 19 2 2217 2750 611409605 611410138 0.000000e+00 870.0
3 TraesCS3B01G610900 chr3D 98.662 299 4 0 2750 3048 611410321 611410619 5.790000e-147 531.0
4 TraesCS3B01G610900 chr3D 97.143 245 7 0 1932 2176 611409360 611409604 6.080000e-112 414.0
5 TraesCS3B01G610900 chr3D 82.904 427 58 11 1 422 611504284 611503868 1.330000e-98 370.0
6 TraesCS3B01G610900 chr3D 74.506 506 75 32 2196 2690 611501166 611501628 1.450000e-38 171.0
7 TraesCS3B01G610900 chr3A 94.706 1530 70 6 1222 2750 746262882 746264401 0.000000e+00 2366.0
8 TraesCS3B01G610900 chr3A 91.341 589 24 10 1 582 746261443 746262011 0.000000e+00 780.0
9 TraesCS3B01G610900 chr3A 97.659 299 7 0 2750 3048 746264585 746264883 5.830000e-142 514.0
10 TraesCS3B01G610900 chr3A 79.634 766 61 45 490 1170 746261979 746262734 2.140000e-126 462.0
11 TraesCS3B01G610900 chr3A 92.593 54 4 0 1167 1220 746262773 746262826 9.060000e-11 78.7
12 TraesCS3B01G610900 chr6D 86.052 466 45 18 3 458 24001615 24002070 1.640000e-132 483.0
13 TraesCS3B01G610900 chr6D 85.991 464 46 14 1 458 16529480 16529030 2.130000e-131 479.0
14 TraesCS3B01G610900 chr6D 84.222 469 54 13 1 458 16307209 16306750 3.610000e-119 438.0
15 TraesCS3B01G610900 chr6D 84.052 464 52 16 1 458 16390051 16389604 7.810000e-116 427.0
16 TraesCS3B01G610900 chr6B 85.361 485 47 18 1 477 38877774 38878242 5.910000e-132 481.0
17 TraesCS3B01G610900 chr6B 85.498 462 48 13 1 458 28256590 28256144 5.950000e-127 464.0
18 TraesCS3B01G610900 chr6B 84.979 466 53 14 1 458 58812436 58812892 9.960000e-125 457.0
19 TraesCS3B01G610900 chr6B 84.648 469 56 13 1 458 59100603 59101066 1.290000e-123 453.0
20 TraesCS3B01G610900 chr6A 84.816 461 56 12 1 458 16720150 16719701 4.630000e-123 451.0
21 TraesCS3B01G610900 chr6A 84.232 482 42 26 1 458 22522716 22523187 3.610000e-119 438.0
22 TraesCS3B01G610900 chr1B 83.439 471 61 16 3 470 28626235 28626691 3.630000e-114 422.0
23 TraesCS3B01G610900 chr7D 82.258 496 52 20 1 474 617735742 617735261 2.200000e-106 396.0
24 TraesCS3B01G610900 chr7D 97.561 41 1 0 1653 1693 52624116 52624156 1.520000e-08 71.3
25 TraesCS3B01G610900 chr5B 97.561 41 1 0 1653 1693 690061076 690061036 1.520000e-08 71.3
26 TraesCS3B01G610900 chr2D 97.561 41 1 0 1653 1693 56184265 56184225 1.520000e-08 71.3
27 TraesCS3B01G610900 chr1A 97.561 41 1 0 1653 1693 47821008 47821048 1.520000e-08 71.3


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 TraesCS3B01G610900 chr3B 829113036 829116083 3047 False 5629.00 5629 100.00000 1 3048 1 chr3B.!!$F1 3047
1 TraesCS3B01G610900 chr3D 611407363 611410619 3256 False 1058.25 2418 95.22625 1 3048 4 chr3D.!!$F2 3047
2 TraesCS3B01G610900 chr3A 746261443 746264883 3440 False 840.14 2366 91.18660 1 3048 5 chr3A.!!$F1 3047

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
216 224 0.033601 AGGGCTGACAGATCTCGTCT 60.034 55.0 19.39 3.79 37.80 4.18 F
1067 1212 0.250081 GGGAAGATGCTGGATCGGAC 60.250 60.0 3.41 0.10 36.04 4.79 F
1473 1727 0.672401 TCCGTCCAGTGAAATTCCGC 60.672 55.0 0.00 0.00 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1120 1265 0.321298 AACCGAACACGAGAATGGGG 60.321 55.000 0.0 0.0 0.00 4.96 R
2032 2323 0.518636 CAGGTCATCCACTGTTTGCG 59.481 55.000 0.0 0.0 35.89 4.85 R
2643 2935 1.072965 AGCTCCCTTGTGCTATATGCC 59.927 52.381 0.0 0.0 39.43 4.40 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
161 162 4.384599 GGTAACCACCCAACCGAC 57.615 61.111 0.00 0.00 39.11 4.79
163 164 1.668793 GTAACCACCCAACCGACCG 60.669 63.158 0.00 0.00 0.00 4.79
164 165 1.836158 TAACCACCCAACCGACCGA 60.836 57.895 0.00 0.00 0.00 4.69
165 166 1.193462 TAACCACCCAACCGACCGAT 61.193 55.000 0.00 0.00 0.00 4.18
166 167 2.125269 CCACCCAACCGACCGATC 60.125 66.667 0.00 0.00 0.00 3.69
167 168 2.656069 CCACCCAACCGACCGATCT 61.656 63.158 0.00 0.00 0.00 2.75
169 170 2.104331 CCCAACCGACCGATCTCG 59.896 66.667 0.00 0.00 39.44 4.04
170 171 2.707849 CCCAACCGACCGATCTCGT 61.708 63.158 3.97 0.00 37.74 4.18
171 172 1.516386 CCAACCGACCGATCTCGTG 60.516 63.158 3.97 0.00 37.74 4.35
212 220 1.739049 CGGAGGGCTGACAGATCTC 59.261 63.158 6.65 11.23 0.00 2.75
213 221 1.739049 GGAGGGCTGACAGATCTCG 59.261 63.158 6.65 0.00 0.00 4.04
214 222 1.040339 GGAGGGCTGACAGATCTCGT 61.040 60.000 6.65 0.00 0.00 4.18
215 223 0.383949 GAGGGCTGACAGATCTCGTC 59.616 60.000 6.65 14.67 0.00 4.20
216 224 0.033601 AGGGCTGACAGATCTCGTCT 60.034 55.000 19.39 3.79 37.80 4.18
217 225 0.383949 GGGCTGACAGATCTCGTCTC 59.616 60.000 19.39 13.49 34.00 3.36
288 296 1.532868 CGCCAAGGACAACAAGAAGAG 59.467 52.381 0.00 0.00 0.00 2.85
417 425 2.435586 CGTGCTGCTCCCCAAGAG 60.436 66.667 0.00 0.00 46.29 2.85
443 451 1.819905 GAGAAGGCCGAGAAGGAGG 59.180 63.158 0.00 0.00 45.00 4.30
468 476 4.344865 GCCCAAGTCGCCCAGGAA 62.345 66.667 0.00 0.00 0.00 3.36
473 481 0.321671 CAAGTCGCCCAGGAAGAAGA 59.678 55.000 0.00 0.00 0.00 2.87
476 484 2.125512 CGCCCAGGAAGAAGACCG 60.126 66.667 0.00 0.00 0.00 4.79
477 485 2.646175 CGCCCAGGAAGAAGACCGA 61.646 63.158 0.00 0.00 0.00 4.69
478 486 1.219393 GCCCAGGAAGAAGACCGAG 59.781 63.158 0.00 0.00 0.00 4.63
479 487 1.258445 GCCCAGGAAGAAGACCGAGA 61.258 60.000 0.00 0.00 0.00 4.04
480 488 1.267121 CCCAGGAAGAAGACCGAGAA 58.733 55.000 0.00 0.00 0.00 2.87
481 489 1.205893 CCCAGGAAGAAGACCGAGAAG 59.794 57.143 0.00 0.00 0.00 2.85
482 490 2.171840 CCAGGAAGAAGACCGAGAAGA 58.828 52.381 0.00 0.00 0.00 2.87
483 491 2.563179 CCAGGAAGAAGACCGAGAAGAA 59.437 50.000 0.00 0.00 0.00 2.52
484 492 3.367910 CCAGGAAGAAGACCGAGAAGAAG 60.368 52.174 0.00 0.00 0.00 2.85
524 532 2.991580 AGAAGACCCCCAAGAAGAAGA 58.008 47.619 0.00 0.00 0.00 2.87
545 592 2.342279 CCGCCGACAAGAAGACCA 59.658 61.111 0.00 0.00 0.00 4.02
600 686 2.192443 CGCCGAGGAGGAGGAGTA 59.808 66.667 0.00 0.00 45.00 2.59
601 687 1.894756 CGCCGAGGAGGAGGAGTAG 60.895 68.421 0.00 0.00 45.00 2.57
604 690 1.479757 GCCGAGGAGGAGGAGTAGAAT 60.480 57.143 0.00 0.00 45.00 2.40
609 695 1.052617 GAGGAGGAGTAGAATGGCCC 58.947 60.000 0.00 0.00 0.00 5.80
610 696 0.400670 AGGAGGAGTAGAATGGCCCC 60.401 60.000 0.00 0.00 0.00 5.80
613 699 1.049289 AGGAGTAGAATGGCCCCGTC 61.049 60.000 0.00 0.00 0.00 4.79
642 728 2.244486 AGTTCTGCATCTGAGAGGGA 57.756 50.000 0.00 0.00 0.00 4.20
648 734 1.331214 GCATCTGAGAGGGAGAGAGG 58.669 60.000 0.00 0.00 0.00 3.69
759 874 3.254166 TGCTGAATTGAAGCTGGAAACTC 59.746 43.478 10.28 0.00 41.42 3.01
801 916 0.888619 TTCTCCGTGTCAATCTCGCT 59.111 50.000 0.00 0.00 0.00 4.93
803 918 2.298610 TCTCCGTGTCAATCTCGCTAT 58.701 47.619 0.00 0.00 0.00 2.97
825 940 3.691049 TTTTGCTGGTTCTTGAAGTCG 57.309 42.857 0.00 0.00 0.00 4.18
826 941 0.944386 TTGCTGGTTCTTGAAGTCGC 59.056 50.000 0.00 0.00 0.00 5.19
827 942 0.884704 TGCTGGTTCTTGAAGTCGCC 60.885 55.000 0.00 0.00 0.00 5.54
828 943 0.603975 GCTGGTTCTTGAAGTCGCCT 60.604 55.000 0.00 0.00 0.00 5.52
829 944 1.433534 CTGGTTCTTGAAGTCGCCTC 58.566 55.000 0.00 0.00 0.00 4.70
871 986 4.503734 CACATTTGTTCGCACAATTTCACT 59.496 37.500 0.43 0.00 42.66 3.41
872 987 4.739716 ACATTTGTTCGCACAATTTCACTC 59.260 37.500 0.43 0.00 42.66 3.51
916 1031 5.582550 GATTTGGCAATAACTAGGTTCAGC 58.417 41.667 0.00 0.00 0.00 4.26
938 1053 1.202592 GGGTGCGGTTGGTGAAATTTT 60.203 47.619 0.00 0.00 0.00 1.82
939 1054 1.864082 GGTGCGGTTGGTGAAATTTTG 59.136 47.619 0.00 0.00 0.00 2.44
947 1063 2.482494 TGGTGAAATTTTGTGGGGGTT 58.518 42.857 0.00 0.00 0.00 4.11
958 1074 0.906775 GTGGGGGTTAACCGATCTGA 59.093 55.000 18.39 0.00 41.60 3.27
995 1128 4.102054 TGGGGATTATTTCTAGGGTTCGTC 59.898 45.833 0.00 0.00 0.00 4.20
1014 1159 2.492773 GGCGATGCTCAATTGGGGG 61.493 63.158 7.59 0.00 0.00 5.40
1044 1189 1.690219 CGCTCCATGCTAGGGTTCCT 61.690 60.000 0.00 0.00 40.11 3.36
1046 1191 1.207791 CTCCATGCTAGGGTTCCTGT 58.792 55.000 0.00 0.00 34.61 4.00
1050 1195 1.281925 ATGCTAGGGTTCCTGTGGGG 61.282 60.000 0.00 0.00 34.61 4.96
1067 1212 0.250081 GGGAAGATGCTGGATCGGAC 60.250 60.000 3.41 0.10 36.04 4.79
1120 1265 1.667724 TCGGAGGTAAGATTCGTCGAC 59.332 52.381 5.18 5.18 0.00 4.20
1175 1331 0.686789 GCTTGGACCCCAATTTGCTT 59.313 50.000 0.00 0.00 43.07 3.91
1220 1418 3.265221 AGTTCCTCAATCATCCTGCTTGA 59.735 43.478 0.00 0.00 32.41 3.02
1243 1495 7.445121 TGATCTGTCTAATCTGAACAAACTGT 58.555 34.615 0.00 0.00 0.00 3.55
1272 1524 6.372659 TGCTAGGAGAAATCTGTTTGAACATC 59.627 38.462 0.00 0.00 38.41 3.06
1309 1563 2.636830 CTGCTGACTTATGGTTCAGGG 58.363 52.381 1.06 0.00 0.00 4.45
1328 1582 1.152830 TGCCTGGGGTTCAGTTTCC 59.847 57.895 0.00 0.00 41.83 3.13
1391 1645 3.387962 TGGAGACCTGCCAGATTTATCT 58.612 45.455 0.00 0.00 37.72 1.98
1392 1646 3.389329 TGGAGACCTGCCAGATTTATCTC 59.611 47.826 0.00 0.00 34.22 2.75
1412 1666 4.160439 TCTCGGTCATGCTAGTTTCTCAAT 59.840 41.667 0.00 0.00 0.00 2.57
1433 1687 2.094390 TCATCCTGCTTGCTGATTTTGC 60.094 45.455 1.05 0.00 0.00 3.68
1434 1688 1.624336 TCCTGCTTGCTGATTTTGCT 58.376 45.000 1.05 0.00 0.00 3.91
1435 1689 1.271379 TCCTGCTTGCTGATTTTGCTG 59.729 47.619 1.05 0.00 0.00 4.41
1473 1727 0.672401 TCCGTCCAGTGAAATTCCGC 60.672 55.000 0.00 0.00 0.00 5.54
1544 1798 4.442073 GCATCTGTGTGAACATTGAACAAC 59.558 41.667 0.00 0.00 0.00 3.32
1549 1803 3.792956 GTGTGAACATTGAACAACTGCAG 59.207 43.478 13.48 13.48 0.00 4.41
1554 1808 2.362077 ACATTGAACAACTGCAGGAACC 59.638 45.455 19.93 3.62 0.00 3.62
1628 1882 1.593196 CGAGTTTTTCAGGCCTGTCA 58.407 50.000 31.58 17.36 0.00 3.58
1631 1885 3.125316 CGAGTTTTTCAGGCCTGTCATAC 59.875 47.826 31.58 23.11 0.00 2.39
1658 1912 2.156343 ACGAAGTTGCTCTCAAGGAC 57.844 50.000 0.00 0.00 37.78 3.85
1673 1927 2.089349 GGACGCGTTCTCTCAGCAC 61.089 63.158 15.53 0.00 0.00 4.40
1698 1952 5.277828 GGCGATGTTATCCAAGGTACAAATC 60.278 44.000 0.00 0.00 0.00 2.17
1773 2027 1.462283 CGCCTGACAGTCAAAGTGATG 59.538 52.381 4.41 0.00 0.00 3.07
1803 2057 0.897863 TGACCGGGCAATCAAAAGGG 60.898 55.000 8.12 0.00 0.00 3.95
1866 2120 1.596727 GCATTGGAGAAGATGAGCGAC 59.403 52.381 0.00 0.00 0.00 5.19
1873 2127 1.944024 AGAAGATGAGCGACGAGGTAG 59.056 52.381 0.00 0.00 0.00 3.18
1976 2267 8.292448 AGTTCTTTTACTTATGCTGACACATTG 58.708 33.333 0.00 0.00 0.00 2.82
2005 2296 4.637534 ACATGATGATTGTTACAGGTGCTC 59.362 41.667 0.00 0.00 0.00 4.26
2032 2323 3.181500 GGAAGAACATACGGGTGCATTTC 60.181 47.826 0.00 0.00 0.00 2.17
2064 2355 0.532573 TGACCTGCTACTGCTGCTAC 59.467 55.000 0.00 0.00 40.48 3.58
2214 2505 6.102663 CGTCAAATAGACCAGTCTTCTGATT 58.897 40.000 5.49 0.00 44.66 2.57
2254 2545 8.070034 TGCCTGTATCATTCTGATTTTTGATT 57.930 30.769 0.00 0.00 38.26 2.57
2310 2601 5.974751 GCTATTTCTCTTCGACTAAGACAGG 59.025 44.000 0.00 0.00 39.36 4.00
2325 2616 9.220767 GACTAAGACAGGAAGTTAATTCATTGT 57.779 33.333 2.46 2.46 39.91 2.71
2386 2678 7.094205 GGGAACAATTTCTGCTCTCATCTTAAA 60.094 37.037 0.00 0.00 31.71 1.52
2392 2684 8.627208 ATTTCTGCTCTCATCTTAAAACTTGA 57.373 30.769 0.00 0.00 0.00 3.02
2433 2725 1.419387 ACCAGCTATCCATCCAGAAGC 59.581 52.381 0.00 0.00 0.00 3.86
2597 2889 5.833406 TGAGAGTTGCATTTCTTCAAACA 57.167 34.783 2.42 0.00 0.00 2.83
2609 2901 7.568134 GCATTTCTTCAAACACACATGATTCAC 60.568 37.037 0.00 0.00 0.00 3.18
2906 3382 9.647797 GAACAATATCGTACATTGGGTATATGA 57.352 33.333 8.71 0.00 37.64 2.15
3034 3510 9.734984 TGCACTGTTGTACTAGAGCTATATATA 57.265 33.333 0.00 0.00 32.72 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 1.519455 GAACAGGGCACGAGATCGG 60.519 63.158 7.22 0.00 44.95 4.18
163 164 2.003301 GAAAGAACAGGGCACGAGATC 58.997 52.381 0.00 0.00 0.00 2.75
164 165 1.625818 AGAAAGAACAGGGCACGAGAT 59.374 47.619 0.00 0.00 0.00 2.75
165 166 1.000955 GAGAAAGAACAGGGCACGAGA 59.999 52.381 0.00 0.00 0.00 4.04
166 167 1.433534 GAGAAAGAACAGGGCACGAG 58.566 55.000 0.00 0.00 0.00 4.18
167 168 0.319555 CGAGAAAGAACAGGGCACGA 60.320 55.000 0.00 0.00 0.00 4.35
169 170 1.869690 GCGAGAAAGAACAGGGCAC 59.130 57.895 0.00 0.00 0.00 5.01
170 171 1.667830 CGCGAGAAAGAACAGGGCA 60.668 57.895 0.00 0.00 0.00 5.36
171 172 3.028366 GCGCGAGAAAGAACAGGGC 62.028 63.158 12.10 0.00 0.00 5.19
212 220 1.328439 CAAAGAACCGAGACGAGACG 58.672 55.000 0.00 0.00 0.00 4.18
213 221 1.268899 TCCAAAGAACCGAGACGAGAC 59.731 52.381 0.00 0.00 0.00 3.36
214 222 1.612676 TCCAAAGAACCGAGACGAGA 58.387 50.000 0.00 0.00 0.00 4.04
215 223 2.263077 CATCCAAAGAACCGAGACGAG 58.737 52.381 0.00 0.00 0.00 4.18
216 224 1.067142 CCATCCAAAGAACCGAGACGA 60.067 52.381 0.00 0.00 0.00 4.20
217 225 1.067142 TCCATCCAAAGAACCGAGACG 60.067 52.381 0.00 0.00 0.00 4.18
385 393 2.282887 ACGGGGTTGATGTTGGGC 60.283 61.111 0.00 0.00 0.00 5.36
465 473 2.675603 GCCTTCTTCTCGGTCTTCTTCC 60.676 54.545 0.00 0.00 0.00 3.46
468 476 0.899019 GGCCTTCTTCTCGGTCTTCT 59.101 55.000 0.00 0.00 0.00 2.85
473 481 3.009714 GGGGGCCTTCTTCTCGGT 61.010 66.667 0.84 0.00 0.00 4.69
476 484 4.491409 GGCGGGGGCCTTCTTCTC 62.491 72.222 0.84 0.00 0.00 2.87
582 668 3.417167 TACTCCTCCTCCTCGGCGG 62.417 68.421 7.21 0.00 39.13 6.13
583 669 1.894756 CTACTCCTCCTCCTCGGCG 60.895 68.421 0.00 0.00 0.00 6.46
584 670 0.106619 TTCTACTCCTCCTCCTCGGC 60.107 60.000 0.00 0.00 0.00 5.54
585 671 2.235016 CATTCTACTCCTCCTCCTCGG 58.765 57.143 0.00 0.00 0.00 4.63
586 672 2.235016 CCATTCTACTCCTCCTCCTCG 58.765 57.143 0.00 0.00 0.00 4.63
587 673 1.967779 GCCATTCTACTCCTCCTCCTC 59.032 57.143 0.00 0.00 0.00 3.71
588 674 1.413808 GGCCATTCTACTCCTCCTCCT 60.414 57.143 0.00 0.00 0.00 3.69
589 675 1.052617 GGCCATTCTACTCCTCCTCC 58.947 60.000 0.00 0.00 0.00 4.30
590 676 1.052617 GGGCCATTCTACTCCTCCTC 58.947 60.000 4.39 0.00 0.00 3.71
591 677 0.400670 GGGGCCATTCTACTCCTCCT 60.401 60.000 4.39 0.00 0.00 3.69
592 678 1.759459 CGGGGCCATTCTACTCCTCC 61.759 65.000 4.39 0.00 0.00 4.30
593 679 1.049289 ACGGGGCCATTCTACTCCTC 61.049 60.000 4.39 0.00 0.00 3.71
594 680 1.003051 ACGGGGCCATTCTACTCCT 59.997 57.895 4.39 0.00 0.00 3.69
595 681 1.446366 GACGGGGCCATTCTACTCC 59.554 63.158 4.39 0.00 0.00 3.85
596 682 1.067582 CGACGGGGCCATTCTACTC 59.932 63.158 4.39 0.00 0.00 2.59
597 683 3.090219 GCGACGGGGCCATTCTACT 62.090 63.158 4.39 0.00 0.00 2.57
598 684 2.588034 GCGACGGGGCCATTCTAC 60.588 66.667 4.39 0.00 0.00 2.59
599 685 4.215742 CGCGACGGGGCCATTCTA 62.216 66.667 4.39 0.00 0.00 2.10
609 695 2.494591 GAACTTAGCGACGCGACGG 61.495 63.158 29.83 16.71 0.00 4.79
610 696 1.511464 AGAACTTAGCGACGCGACG 60.511 57.895 25.73 25.73 0.00 5.12
613 699 1.413767 ATGCAGAACTTAGCGACGCG 61.414 55.000 15.18 3.53 0.00 6.01
621 707 3.703556 CTCCCTCTCAGATGCAGAACTTA 59.296 47.826 0.00 0.00 0.00 2.24
622 708 2.500910 CTCCCTCTCAGATGCAGAACTT 59.499 50.000 0.00 0.00 0.00 2.66
642 728 3.559069 CATGCTCTCTCTCTTCCTCTCT 58.441 50.000 0.00 0.00 0.00 3.10
648 734 2.299867 GGATCCCATGCTCTCTCTCTTC 59.700 54.545 0.00 0.00 0.00 2.87
759 874 4.273480 AGATTGGAATTGGCTAAACGATCG 59.727 41.667 14.88 14.88 0.00 3.69
820 935 1.686110 AAGGGGATCGAGGCGACTT 60.686 57.895 0.00 0.00 44.43 3.01
822 937 2.107141 CAAGGGGATCGAGGCGAC 59.893 66.667 0.00 0.00 39.18 5.19
824 939 1.521681 GAACAAGGGGATCGAGGCG 60.522 63.158 0.00 0.00 0.00 5.52
825 940 1.521681 CGAACAAGGGGATCGAGGC 60.522 63.158 0.00 0.00 38.82 4.70
826 941 0.179108 GACGAACAAGGGGATCGAGG 60.179 60.000 1.03 0.00 39.73 4.63
827 942 0.818296 AGACGAACAAGGGGATCGAG 59.182 55.000 1.03 0.00 39.73 4.04
828 943 0.530744 CAGACGAACAAGGGGATCGA 59.469 55.000 1.03 0.00 39.73 3.59
829 944 1.084370 GCAGACGAACAAGGGGATCG 61.084 60.000 0.00 0.00 42.05 3.69
871 986 0.688487 CCCCAAGAACACCTAACCGA 59.312 55.000 0.00 0.00 0.00 4.69
872 987 0.322187 CCCCCAAGAACACCTAACCG 60.322 60.000 0.00 0.00 0.00 4.44
916 1031 4.939368 TTCACCAACCGCACCCCG 62.939 66.667 0.00 0.00 0.00 5.73
928 1043 4.382291 GTTAACCCCCACAAAATTTCACC 58.618 43.478 0.00 0.00 0.00 4.02
938 1053 0.616371 CAGATCGGTTAACCCCCACA 59.384 55.000 19.09 0.00 0.00 4.17
939 1054 0.906775 TCAGATCGGTTAACCCCCAC 59.093 55.000 19.09 8.14 0.00 4.61
947 1063 1.691482 CCCTTCCCCTCAGATCGGTTA 60.691 57.143 0.00 0.00 0.00 2.85
958 1074 2.378522 CCCAGATCCCCTTCCCCT 59.621 66.667 0.00 0.00 0.00 4.79
995 1128 2.717485 CCCAATTGAGCATCGCCG 59.283 61.111 7.12 0.00 38.61 6.46
1044 1189 0.548031 GATCCAGCATCTTCCCCACA 59.452 55.000 0.00 0.00 0.00 4.17
1046 1191 1.699054 CCGATCCAGCATCTTCCCCA 61.699 60.000 0.00 0.00 0.00 4.96
1050 1195 0.598680 CGGTCCGATCCAGCATCTTC 60.599 60.000 4.91 0.00 0.00 2.87
1054 1199 4.241555 GGCGGTCCGATCCAGCAT 62.242 66.667 17.49 0.00 0.00 3.79
1067 1212 2.809601 CTGACGAGAAACCGGCGG 60.810 66.667 27.06 27.06 41.26 6.13
1120 1265 0.321298 AACCGAACACGAGAATGGGG 60.321 55.000 0.00 0.00 0.00 4.96
1175 1331 8.079211 ACTAGCATGATCTTCCTAAGTTTGTA 57.921 34.615 0.00 0.00 0.00 2.41
1220 1418 9.429359 CTTACAGTTTGTTCAGATTAGACAGAT 57.571 33.333 0.00 0.00 0.00 2.90
1243 1495 7.004555 TCAAACAGATTTCTCCTAGCACTTA 57.995 36.000 0.00 0.00 0.00 2.24
1391 1645 3.953712 TTGAGAAACTAGCATGACCGA 57.046 42.857 0.00 0.00 0.00 4.69
1392 1646 4.183865 TGATTGAGAAACTAGCATGACCG 58.816 43.478 0.00 0.00 0.00 4.79
1412 1666 2.094390 GCAAAATCAGCAAGCAGGATGA 60.094 45.455 0.00 0.00 39.69 2.92
1433 1687 6.017934 ACGGAATAAATACATTGTGCTAGCAG 60.018 38.462 20.03 9.07 0.00 4.24
1434 1688 5.820423 ACGGAATAAATACATTGTGCTAGCA 59.180 36.000 14.93 14.93 0.00 3.49
1435 1689 6.300354 ACGGAATAAATACATTGTGCTAGC 57.700 37.500 8.10 8.10 0.00 3.42
1455 1709 1.794222 GCGGAATTTCACTGGACGG 59.206 57.895 0.00 0.00 0.00 4.79
1519 1773 2.493035 TCAATGTTCACACAGATGCGT 58.507 42.857 0.00 0.00 35.94 5.24
1520 1774 3.228749 GTTCAATGTTCACACAGATGCG 58.771 45.455 0.00 0.00 35.94 4.73
1521 1775 4.227512 TGTTCAATGTTCACACAGATGC 57.772 40.909 0.00 0.00 35.94 3.91
1522 1776 5.684184 CAGTTGTTCAATGTTCACACAGATG 59.316 40.000 0.00 0.00 35.94 2.90
1544 1798 1.597854 TCAAGCACGGTTCCTGCAG 60.598 57.895 6.78 6.78 37.08 4.41
1566 1820 5.452078 TCAAAACATCCTGAACCATTCAC 57.548 39.130 0.00 0.00 35.46 3.18
1628 1882 1.796459 GCAACTTCGTTGGTGTCGTAT 59.204 47.619 8.60 0.00 42.99 3.06
1631 1885 4.893241 GCAACTTCGTTGGTGTCG 57.107 55.556 8.60 0.00 42.99 4.35
1640 1894 1.063806 CGTCCTTGAGAGCAACTTCG 58.936 55.000 0.00 0.00 0.00 3.79
1658 1912 3.175240 CCGTGCTGAGAGAACGCG 61.175 66.667 3.53 3.53 45.75 6.01
1673 1927 2.132762 GTACCTTGGATAACATCGCCG 58.867 52.381 0.00 0.00 0.00 6.46
1698 1952 8.037382 TCAGCAAAAAGATTCAGAACAGATAG 57.963 34.615 0.00 0.00 0.00 2.08
1803 2057 2.728318 GGAGAACTTGACGAAACCGTAC 59.272 50.000 0.00 0.00 40.80 3.67
1866 2120 2.972625 TGAAGCACAATTCCTACCTCG 58.027 47.619 0.00 0.00 0.00 4.63
1873 2127 4.159135 ACAGAATCCATGAAGCACAATTCC 59.841 41.667 0.00 0.00 0.00 3.01
1976 2267 5.163622 CCTGTAACAATCATCATGTGGGAAC 60.164 44.000 0.00 0.00 0.00 3.62
2005 2296 1.138266 ACCCGTATGTTCTTCCCATCG 59.862 52.381 0.00 0.00 0.00 3.84
2032 2323 0.518636 CAGGTCATCCACTGTTTGCG 59.481 55.000 0.00 0.00 35.89 4.85
2064 2355 4.302455 CGGATAAGTACCTTGCTCATCTG 58.698 47.826 0.00 0.00 0.00 2.90
2191 2482 7.913674 AAATCAGAAGACTGGTCTATTTGAC 57.086 36.000 3.54 0.00 43.60 3.18
2214 2505 4.935352 ACAGGCAATGTCAAGCTAAAAA 57.065 36.364 0.00 0.00 37.75 1.94
2254 2545 3.714798 AGGTGTTCCTCTGGTTTTCAGTA 59.285 43.478 0.00 0.00 40.58 2.74
2290 2581 5.535406 ACTTCCTGTCTTAGTCGAAGAGAAA 59.465 40.000 0.00 0.00 45.06 2.52
2371 2663 9.932699 CATATTCAAGTTTTAAGATGAGAGCAG 57.067 33.333 0.00 0.00 0.00 4.24
2392 2684 3.576078 TTCCATCGGACTTGCCATATT 57.424 42.857 0.00 0.00 35.94 1.28
2433 2725 5.204833 GCTTGCCACAACATACATAATACG 58.795 41.667 0.00 0.00 0.00 3.06
2527 2819 5.243730 AGCTCAAATTTTACAGCTGCCTTTA 59.756 36.000 15.27 0.00 40.79 1.85
2530 2822 3.160269 AGCTCAAATTTTACAGCTGCCT 58.840 40.909 15.27 0.00 40.79 4.75
2564 2856 3.937814 TGCAACTCTCATGTCGGTAAAT 58.062 40.909 0.00 0.00 0.00 1.40
2597 2889 4.265904 TGTTCCGTAGTGAATCATGTGT 57.734 40.909 0.00 0.00 0.00 3.72
2609 2901 7.371159 TGAGCTAAATATGAGATGTTCCGTAG 58.629 38.462 0.00 0.00 0.00 3.51
2643 2935 1.072965 AGCTCCCTTGTGCTATATGCC 59.927 52.381 0.00 0.00 39.43 4.40


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

AutoCloner maintained by Alex Coulton.