Multiple sequence alignment - TraesCS2D01G173300

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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 TraesCS2D01G173300 chr2D 100.000 3136 0 0 1 3136 117126617 117123482 0.000000e+00 5792.0
1 TraesCS2D01G173300 chr2A 92.659 1798 88 21 547 2335 118466536 118464774 0.000000e+00 2549.0
2 TraesCS2D01G173300 chr2A 91.254 343 11 10 2639 2971 118464498 118464165 1.720000e-122 449.0
3 TraesCS2D01G173300 chr2A 91.342 231 15 4 2333 2559 118464747 118464518 8.450000e-81 311.0
4 TraesCS2D01G173300 chr2A 94.495 109 6 0 3028 3136 118462060 118461952 5.380000e-38 169.0
5 TraesCS2D01G173300 chr2A 85.075 134 7 6 3004 3136 118463900 118463779 1.180000e-24 124.0
6 TraesCS2D01G173300 chr2B 94.317 1531 42 25 811 2336 167477139 167475649 0.000000e+00 2303.0
7 TraesCS2D01G173300 chr2B 94.425 574 14 6 2342 2909 167475595 167475034 0.000000e+00 867.0
8 TraesCS2D01G173300 chr2B 85.153 458 61 4 6 461 167478468 167478016 2.200000e-126 462.0
9 TraesCS2D01G173300 chr2B 82.821 390 34 19 444 820 167477686 167477317 5.050000e-83 318.0
10 TraesCS2D01G173300 chr2B 88.095 168 14 5 2973 3136 167474809 167474644 8.870000e-46 195.0
11 TraesCS2D01G173300 chr2B 87.500 72 3 1 2907 2972 167474911 167474840 9.330000e-11 78.7


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 TraesCS2D01G173300 chr2D 117123482 117126617 3135 True 5792.00 5792 100.0000 1 3136 1 chr2D.!!$R1 3135
1 TraesCS2D01G173300 chr2A 118461952 118466536 4584 True 720.40 2549 90.9650 547 3136 5 chr2A.!!$R1 2589
2 TraesCS2D01G173300 chr2B 167474644 167478468 3824 True 703.95 2303 88.7185 6 3136 6 chr2B.!!$R1 3130

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
262 263 0.040425 GTTTTCGTCATGCAAGCGGT 60.040 50.0 0.00 0.00 0.00 5.68 F
382 384 0.107654 CAAGTGGTCCGGATTCTCCC 60.108 60.0 7.81 3.81 31.13 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2571 0.177373 TCGACGAGGAGTAGCTGCTA 59.823 55.0 3.57 5.02 30.82 3.49 R
2336 2904 0.462759 GTCGCCCAATCTCTCCAAGG 60.463 60.0 0.00 0.00 0.00 3.61 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
22 23 0.869730 CAATTGTTGCTTTGGGCTGC 59.130 50.000 0.00 0.00 42.39 5.25
23 24 0.760572 AATTGTTGCTTTGGGCTGCT 59.239 45.000 0.00 0.00 42.39 4.24
24 25 1.631405 ATTGTTGCTTTGGGCTGCTA 58.369 45.000 0.00 0.00 42.39 3.49
36 37 4.027674 TGGGCTGCTATTCTTTGTGTTA 57.972 40.909 0.00 0.00 0.00 2.41
42 43 6.016777 GGCTGCTATTCTTTGTGTTATATGCT 60.017 38.462 0.00 0.00 0.00 3.79
43 44 7.173218 GGCTGCTATTCTTTGTGTTATATGCTA 59.827 37.037 0.00 0.00 0.00 3.49
94 95 8.772705 TGATTTCTTTTGTATTTCATTGTTGCC 58.227 29.630 0.00 0.00 0.00 4.52
103 104 7.215789 TGTATTTCATTGTTGCCTTTGATTGT 58.784 30.769 0.00 0.00 0.00 2.71
123 124 9.995003 TGATTGTAGAAATTTGGTATTTGCTTT 57.005 25.926 0.00 0.00 0.00 3.51
143 144 8.865590 TGCTTTACCAAACTTAACAAATCTTC 57.134 30.769 0.00 0.00 0.00 2.87
154 155 1.209747 ACAAATCTTCTACCGGCCCTC 59.790 52.381 0.00 0.00 0.00 4.30
157 158 1.403687 ATCTTCTACCGGCCCTCTGC 61.404 60.000 0.00 0.00 40.16 4.26
162 163 1.899437 CTACCGGCCCTCTGCTTTCA 61.899 60.000 0.00 0.00 40.92 2.69
169 170 2.012673 GCCCTCTGCTTTCAGTATGTG 58.987 52.381 0.00 0.00 41.10 3.21
171 172 3.679389 CCCTCTGCTTTCAGTATGTGTT 58.321 45.455 0.00 0.00 41.10 3.32
180 181 3.526931 TCAGTATGTGTTCTGCTAGGC 57.473 47.619 0.00 0.00 37.40 3.93
187 188 4.351874 TGTGTTCTGCTAGGCTAAAAGT 57.648 40.909 0.00 0.00 0.00 2.66
195 196 8.565416 GTTCTGCTAGGCTAAAAGTTTAAGAAA 58.435 33.333 0.00 0.00 0.00 2.52
198 199 9.346725 CTGCTAGGCTAAAAGTTTAAGAAAATG 57.653 33.333 0.00 0.00 0.00 2.32
249 250 5.666969 TCAACATTAGACAGTGGTTTTCG 57.333 39.130 0.00 0.00 0.00 3.46
250 251 5.120399 TCAACATTAGACAGTGGTTTTCGT 58.880 37.500 0.00 0.00 0.00 3.85
261 262 0.729140 GGTTTTCGTCATGCAAGCGG 60.729 55.000 0.00 0.00 0.00 5.52
262 263 0.040425 GTTTTCGTCATGCAAGCGGT 60.040 50.000 0.00 0.00 0.00 5.68
263 264 0.237235 TTTTCGTCATGCAAGCGGTC 59.763 50.000 0.00 0.00 0.00 4.79
264 265 1.896339 TTTCGTCATGCAAGCGGTCG 61.896 55.000 0.00 0.00 0.00 4.79
285 286 2.796032 GCCCGCAAGACATGAATTAAGC 60.796 50.000 0.00 0.00 43.02 3.09
289 290 4.335315 CCGCAAGACATGAATTAAGCCTAA 59.665 41.667 0.00 0.00 43.02 2.69
293 294 7.254761 CGCAAGACATGAATTAAGCCTAACATA 60.255 37.037 0.00 0.00 43.02 2.29
333 335 0.248289 TAGTGTACTTTGGGCCTCGC 59.752 55.000 4.53 0.00 0.00 5.03
371 373 1.598701 GCTTGCATCCCCAAGTGGTC 61.599 60.000 0.00 0.00 43.17 4.02
372 374 0.967380 CTTGCATCCCCAAGTGGTCC 60.967 60.000 0.00 0.00 37.89 4.46
374 376 2.272146 CATCCCCAAGTGGTCCGG 59.728 66.667 0.00 0.00 0.00 5.14
382 384 0.107654 CAAGTGGTCCGGATTCTCCC 60.108 60.000 7.81 3.81 31.13 4.30
384 386 1.689582 GTGGTCCGGATTCTCCCCT 60.690 63.158 7.81 0.00 31.13 4.79
386 388 0.549169 TGGTCCGGATTCTCCCCTTT 60.549 55.000 7.81 0.00 31.13 3.11
391 393 1.004277 CCGGATTCTCCCCTTTTGTCA 59.996 52.381 0.00 0.00 31.13 3.58
392 394 2.359900 CGGATTCTCCCCTTTTGTCAG 58.640 52.381 0.00 0.00 31.13 3.51
398 400 5.852282 TTCTCCCCTTTTGTCAGAAAAAG 57.148 39.130 3.05 3.05 43.67 2.27
416 418 9.369904 CAGAAAAAGGAACAAGAAAATTTGAGA 57.630 29.630 0.00 0.00 0.00 3.27
428 430 7.941795 AGAAAATTTGAGACTTGAATTGCAG 57.058 32.000 0.00 0.00 0.00 4.41
447 449 5.316167 TGCAGGAAAGCTGAGAAAGATTTA 58.684 37.500 0.00 0.00 44.42 1.40
448 450 5.413833 TGCAGGAAAGCTGAGAAAGATTTAG 59.586 40.000 0.00 0.00 44.42 1.85
449 451 5.645497 GCAGGAAAGCTGAGAAAGATTTAGA 59.355 40.000 0.00 0.00 44.42 2.10
456 805 8.414629 AAGCTGAGAAAGATTTAGACCAAAAT 57.585 30.769 0.00 0.00 27.04 1.82
457 806 8.414629 AGCTGAGAAAGATTTAGACCAAAATT 57.585 30.769 0.00 0.00 0.00 1.82
493 842 2.252714 TGGACTTTTTATTGTGGGGGC 58.747 47.619 0.00 0.00 0.00 5.80
509 858 5.046231 TGTGGGGGCAAATTTTAATCCTTAC 60.046 40.000 0.00 0.00 0.00 2.34
514 863 6.183360 GGGGCAAATTTTAATCCTTACTCTCC 60.183 42.308 0.00 0.00 0.00 3.71
515 864 6.379988 GGGCAAATTTTAATCCTTACTCTCCA 59.620 38.462 0.00 0.00 0.00 3.86
516 865 7.093509 GGGCAAATTTTAATCCTTACTCTCCAA 60.094 37.037 0.00 0.00 0.00 3.53
517 866 8.478066 GGCAAATTTTAATCCTTACTCTCCAAT 58.522 33.333 0.00 0.00 0.00 3.16
518 867 9.875691 GCAAATTTTAATCCTTACTCTCCAATT 57.124 29.630 0.00 0.00 0.00 2.32
522 871 9.981460 ATTTTAATCCTTACTCTCCAATTCTGT 57.019 29.630 0.00 0.00 0.00 3.41
528 878 6.500751 TCCTTACTCTCCAATTCTGTTTACCT 59.499 38.462 0.00 0.00 0.00 3.08
560 910 9.160496 ACTTCTGTGTGATCATTAATCTTCTTC 57.840 33.333 0.00 0.00 35.24 2.87
570 920 9.766277 GATCATTAATCTTCTTCAGTTGTTGAC 57.234 33.333 0.00 0.00 34.94 3.18
571 921 8.675705 TCATTAATCTTCTTCAGTTGTTGACA 57.324 30.769 0.00 0.00 34.94 3.58
573 923 8.562892 CATTAATCTTCTTCAGTTGTTGACAGT 58.437 33.333 0.00 0.00 34.94 3.55
574 924 8.506168 TTAATCTTCTTCAGTTGTTGACAGTT 57.494 30.769 0.00 0.00 34.94 3.16
575 925 6.610741 ATCTTCTTCAGTTGTTGACAGTTC 57.389 37.500 0.00 0.00 34.94 3.01
576 926 5.734720 TCTTCTTCAGTTGTTGACAGTTCT 58.265 37.500 0.00 0.00 34.94 3.01
619 969 5.304211 CGTTTATTCCAAACGGTTTTGTG 57.696 39.130 13.02 0.00 46.39 3.33
626 976 3.066064 TCCAAACGGTTTTGTGTGATCAG 59.934 43.478 2.79 0.00 40.61 2.90
631 989 5.418310 ACGGTTTTGTGTGATCAGTAAAG 57.582 39.130 0.00 0.00 0.00 1.85
632 990 4.879545 ACGGTTTTGTGTGATCAGTAAAGT 59.120 37.500 0.00 0.00 0.00 2.66
661 1019 7.875316 ACAATTCATCTCGCTATATACACAC 57.125 36.000 0.00 0.00 0.00 3.82
712 1071 3.285215 GCTAGCGGCTGCATGCAT 61.285 61.111 22.97 8.57 46.23 3.96
875 1425 0.547712 CCCCCTCTCTCCCTTCAACA 60.548 60.000 0.00 0.00 0.00 3.33
942 1496 1.221635 TCCTCTCTCCCTCTCTCCAG 58.778 60.000 0.00 0.00 0.00 3.86
1013 1567 7.382759 CGGAGGCATCTATCTTTAAAGAAGTAC 59.617 40.741 21.26 9.27 38.77 2.73
1018 1578 9.050601 GCATCTATCTTTAAAGAAGTACAGCAT 57.949 33.333 21.26 4.88 38.77 3.79
1021 1581 9.809096 TCTATCTTTAAAGAAGTACAGCATCAG 57.191 33.333 21.26 0.00 38.77 2.90
1022 1582 9.809096 CTATCTTTAAAGAAGTACAGCATCAGA 57.191 33.333 21.26 0.00 38.77 3.27
1024 1584 8.539770 TCTTTAAAGAAGTACAGCATCAGAAG 57.460 34.615 15.57 0.00 30.73 2.85
1025 1585 8.367911 TCTTTAAAGAAGTACAGCATCAGAAGA 58.632 33.333 15.57 0.00 30.73 2.87
1026 1586 8.539770 TTTAAAGAAGTACAGCATCAGAAGAG 57.460 34.615 0.00 0.00 0.00 2.85
1027 1587 4.734398 AGAAGTACAGCATCAGAAGAGG 57.266 45.455 0.00 0.00 0.00 3.69
1032 1592 2.109774 ACAGCATCAGAAGAGGAGAGG 58.890 52.381 0.00 0.00 0.00 3.69
1054 1614 3.074999 GCAGAGGCGGAGAGTGAGG 62.075 68.421 0.00 0.00 0.00 3.86
1055 1615 1.379176 CAGAGGCGGAGAGTGAGGA 60.379 63.158 0.00 0.00 0.00 3.71
1291 1854 2.431942 TTCGACTTCGCCTTCGGC 60.432 61.111 0.00 0.00 46.75 5.54
2336 2904 2.417719 ACTCGAGCACACCTTGAATTC 58.582 47.619 13.61 0.00 33.54 2.17
2339 2925 2.154462 CGAGCACACCTTGAATTCCTT 58.846 47.619 2.27 0.00 0.00 3.36
2344 2960 3.754965 CACACCTTGAATTCCTTGGAGA 58.245 45.455 13.23 0.00 0.00 3.71
2349 2965 5.125097 CACCTTGAATTCCTTGGAGAGATTG 59.875 44.000 13.23 0.18 0.00 2.67
2372 2988 2.361610 CCAAACCCTGCATCGGCT 60.362 61.111 0.00 0.00 41.91 5.52
2379 2995 1.589993 CCTGCATCGGCTCACGTAG 60.590 63.158 0.00 0.00 44.69 3.51
2602 3226 3.181524 CGAACTGTCACAACTGTTTCGTT 60.182 43.478 5.77 0.00 44.59 3.85
2733 3357 2.700897 AGTAACCGGCATGATTAGAGCT 59.299 45.455 0.00 0.00 0.00 4.09
2735 3359 3.838244 AACCGGCATGATTAGAGCTTA 57.162 42.857 0.00 0.00 0.00 3.09
2736 3360 3.393089 ACCGGCATGATTAGAGCTTAG 57.607 47.619 0.00 0.00 0.00 2.18
2737 3361 2.072298 CCGGCATGATTAGAGCTTAGC 58.928 52.381 0.00 0.00 0.00 3.09
2738 3362 2.289320 CCGGCATGATTAGAGCTTAGCT 60.289 50.000 6.37 6.37 43.88 3.32
2739 3363 3.056536 CCGGCATGATTAGAGCTTAGCTA 60.057 47.826 6.75 0.00 39.88 3.32
2740 3364 4.172505 CGGCATGATTAGAGCTTAGCTAG 58.827 47.826 6.75 0.00 39.88 3.42
2782 3406 6.259167 TGAGGTGTTGATGTGTTTGTTACTAC 59.741 38.462 0.00 0.00 0.00 2.73
2783 3407 6.354130 AGGTGTTGATGTGTTTGTTACTACT 58.646 36.000 0.00 0.00 0.00 2.57
2784 3408 7.502696 AGGTGTTGATGTGTTTGTTACTACTA 58.497 34.615 0.00 0.00 0.00 1.82
2785 3409 7.656137 AGGTGTTGATGTGTTTGTTACTACTAG 59.344 37.037 0.00 0.00 0.00 2.57
2786 3410 7.440255 GGTGTTGATGTGTTTGTTACTACTAGT 59.560 37.037 0.00 0.00 0.00 2.57
2787 3411 9.467258 GTGTTGATGTGTTTGTTACTACTAGTA 57.533 33.333 1.89 1.89 0.00 1.82
2897 3521 6.566197 TTGCAAAGATTCTCTTTCTTCTCC 57.434 37.500 0.00 0.00 42.60 3.71
2901 3525 6.348376 GCAAAGATTCTCTTTCTTCTCCACTG 60.348 42.308 0.00 0.00 42.60 3.66
2909 3533 4.164221 TCTTTCTTCTCCACTGGACAAGTT 59.836 41.667 11.63 0.00 36.83 2.66
2947 3696 4.018506 TCTCTGGCCTGGATTTCAATTGTA 60.019 41.667 10.07 0.00 0.00 2.41
2972 3727 1.134220 TGTCTTGGTTGGGACTGTGAC 60.134 52.381 0.00 0.00 34.01 3.67
2976 3731 0.462937 TGGTTGGGACTGTGACGTTG 60.463 55.000 0.00 0.00 0.00 4.10
2977 3732 1.164041 GGTTGGGACTGTGACGTTGG 61.164 60.000 0.00 0.00 0.00 3.77
2979 3734 0.542333 TTGGGACTGTGACGTTGGAA 59.458 50.000 0.00 0.00 0.00 3.53
2980 3735 0.105964 TGGGACTGTGACGTTGGAAG 59.894 55.000 0.00 0.00 0.00 3.46
2981 3736 0.391597 GGGACTGTGACGTTGGAAGA 59.608 55.000 0.00 0.00 0.00 2.87
3014 4007 0.253044 TGCTGCCTGGAATGTACTCC 59.747 55.000 0.00 0.00 35.88 3.85
3113 5922 2.011947 ACATCATCATGAACGGTGCTG 58.988 47.619 0.00 0.00 33.72 4.41
3116 5925 3.817709 TCATCATGAACGGTGCTGATA 57.182 42.857 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.256631 ACACAAAGAATAGCAGCCCAAAG 59.743 43.478 0.00 0.00 0.00 2.77
18 19 6.963796 AGCATATAACACAAAGAATAGCAGC 58.036 36.000 0.00 0.00 0.00 5.25
23 24 9.777297 TGAGCATAGCATATAACACAAAGAATA 57.223 29.630 0.00 0.00 0.00 1.75
24 25 8.681486 TGAGCATAGCATATAACACAAAGAAT 57.319 30.769 0.00 0.00 0.00 2.40
36 37 8.781196 CAACACTTTAAGATGAGCATAGCATAT 58.219 33.333 0.00 0.00 0.00 1.78
42 43 6.816134 TTGCAACACTTTAAGATGAGCATA 57.184 33.333 0.00 0.76 33.11 3.14
43 44 5.710513 TTGCAACACTTTAAGATGAGCAT 57.289 34.783 0.00 0.00 33.11 3.79
76 77 8.557864 CAATCAAAGGCAACAATGAAATACAAA 58.442 29.630 0.00 0.00 37.06 2.83
77 78 7.714377 ACAATCAAAGGCAACAATGAAATACAA 59.286 29.630 0.00 0.00 37.06 2.41
123 124 7.388500 CCGGTAGAAGATTTGTTAAGTTTGGTA 59.612 37.037 0.00 0.00 0.00 3.25
125 126 6.608610 CCGGTAGAAGATTTGTTAAGTTTGG 58.391 40.000 0.00 0.00 0.00 3.28
130 131 3.626217 GGGCCGGTAGAAGATTTGTTAAG 59.374 47.826 1.90 0.00 0.00 1.85
135 136 1.486726 AGAGGGCCGGTAGAAGATTTG 59.513 52.381 1.90 0.00 0.00 2.32
143 144 1.153349 GAAAGCAGAGGGCCGGTAG 60.153 63.158 1.90 0.00 46.50 3.18
146 147 1.899437 TACTGAAAGCAGAGGGCCGG 61.899 60.000 0.00 0.00 45.17 6.13
147 148 0.179000 ATACTGAAAGCAGAGGGCCG 59.821 55.000 0.00 0.00 45.17 6.13
157 158 4.331168 GCCTAGCAGAACACATACTGAAAG 59.669 45.833 0.00 0.00 42.29 2.62
162 163 5.677319 TTTAGCCTAGCAGAACACATACT 57.323 39.130 0.00 0.00 0.00 2.12
169 170 7.668525 TCTTAAACTTTTAGCCTAGCAGAAC 57.331 36.000 0.00 0.00 0.00 3.01
171 172 8.685838 TTTTCTTAAACTTTTAGCCTAGCAGA 57.314 30.769 0.00 0.00 0.00 4.26
195 196 7.278875 TGGAAAAACTATTGCAAAGGAACATT 58.721 30.769 1.71 0.00 0.00 2.71
198 199 7.095229 GGAATGGAAAAACTATTGCAAAGGAAC 60.095 37.037 1.71 0.00 37.63 3.62
249 250 4.166011 GGCGACCGCTTGCATGAC 62.166 66.667 14.25 0.00 41.60 3.06
261 262 1.369091 ATTCATGTCTTGCGGGCGAC 61.369 55.000 0.00 0.00 0.00 5.19
262 263 0.676466 AATTCATGTCTTGCGGGCGA 60.676 50.000 0.00 0.00 0.00 5.54
263 264 1.013596 TAATTCATGTCTTGCGGGCG 58.986 50.000 0.00 0.00 0.00 6.13
264 265 2.796032 GCTTAATTCATGTCTTGCGGGC 60.796 50.000 0.00 0.00 0.00 6.13
285 286 9.612620 CTTTGCTACTTCAGTTTTTATGTTAGG 57.387 33.333 0.00 0.00 0.00 2.69
293 294 8.903820 ACACTAATCTTTGCTACTTCAGTTTTT 58.096 29.630 0.00 0.00 0.00 1.94
298 299 8.764524 AAGTACACTAATCTTTGCTACTTCAG 57.235 34.615 0.00 0.00 0.00 3.02
299 300 8.988934 CAAAGTACACTAATCTTTGCTACTTCA 58.011 33.333 0.00 0.00 40.53 3.02
300 301 8.443937 CCAAAGTACACTAATCTTTGCTACTTC 58.556 37.037 10.22 0.00 43.49 3.01
306 308 4.380550 GGCCCAAAGTACACTAATCTTTGC 60.381 45.833 10.22 2.39 43.49 3.68
351 353 2.703798 CCACTTGGGGATGCAAGCG 61.704 63.158 0.00 0.00 32.03 4.68
372 374 9.595247 CTTTTTCTGACAAAAGGGGAGAATCCG 62.595 44.444 12.93 0.00 44.11 4.18
374 376 6.405278 TTTTTCTGACAAAAGGGGAGAATC 57.595 37.500 0.00 0.00 0.00 2.52
384 386 8.894768 TTTTCTTGTTCCTTTTTCTGACAAAA 57.105 26.923 0.00 0.00 30.72 2.44
386 388 9.500785 AAATTTTCTTGTTCCTTTTTCTGACAA 57.499 25.926 0.00 0.00 0.00 3.18
391 393 9.371136 GTCTCAAATTTTCTTGTTCCTTTTTCT 57.629 29.630 0.00 0.00 0.00 2.52
392 394 9.371136 AGTCTCAAATTTTCTTGTTCCTTTTTC 57.629 29.630 0.00 0.00 0.00 2.29
398 400 8.877808 ATTCAAGTCTCAAATTTTCTTGTTCC 57.122 30.769 15.38 0.00 37.39 3.62
400 402 8.606602 GCAATTCAAGTCTCAAATTTTCTTGTT 58.393 29.630 15.38 6.91 37.39 2.83
402 404 8.133754 TGCAATTCAAGTCTCAAATTTTCTTG 57.866 30.769 12.20 12.20 37.44 3.02
405 407 6.925165 TCCTGCAATTCAAGTCTCAAATTTTC 59.075 34.615 0.00 0.00 0.00 2.29
406 408 6.819284 TCCTGCAATTCAAGTCTCAAATTTT 58.181 32.000 0.00 0.00 0.00 1.82
416 418 3.225104 TCAGCTTTCCTGCAATTCAAGT 58.775 40.909 0.00 0.00 41.50 3.16
428 430 5.940470 TGGTCTAAATCTTTCTCAGCTTTCC 59.060 40.000 0.00 0.00 0.00 3.13
470 819 3.643792 CCCCCACAATAAAAAGTCCAACA 59.356 43.478 0.00 0.00 0.00 3.33
472 821 2.635427 GCCCCCACAATAAAAAGTCCAA 59.365 45.455 0.00 0.00 0.00 3.53
473 822 2.252714 GCCCCCACAATAAAAAGTCCA 58.747 47.619 0.00 0.00 0.00 4.02
474 823 2.252714 TGCCCCCACAATAAAAAGTCC 58.747 47.619 0.00 0.00 0.00 3.85
475 824 4.344359 TTTGCCCCCACAATAAAAAGTC 57.656 40.909 0.00 0.00 0.00 3.01
476 825 4.991789 ATTTGCCCCCACAATAAAAAGT 57.008 36.364 0.00 0.00 0.00 2.66
477 826 6.647334 AAAATTTGCCCCCACAATAAAAAG 57.353 33.333 0.00 0.00 0.00 2.27
478 827 8.712228 ATTAAAATTTGCCCCCACAATAAAAA 57.288 26.923 0.00 0.00 0.00 1.94
483 832 4.539696 AGGATTAAAATTTGCCCCCACAAT 59.460 37.500 0.00 0.00 0.00 2.71
485 834 3.525862 AGGATTAAAATTTGCCCCCACA 58.474 40.909 0.00 0.00 0.00 4.17
486 835 4.568072 AAGGATTAAAATTTGCCCCCAC 57.432 40.909 0.00 0.00 0.00 4.61
487 836 5.346270 AGTAAGGATTAAAATTTGCCCCCA 58.654 37.500 0.00 0.00 28.70 4.96
489 838 6.183360 GGAGAGTAAGGATTAAAATTTGCCCC 60.183 42.308 0.00 0.00 28.70 5.80
538 888 8.489990 ACTGAAGAAGATTAATGATCACACAG 57.510 34.615 0.00 0.00 37.22 3.66
540 890 8.725148 ACAACTGAAGAAGATTAATGATCACAC 58.275 33.333 0.00 0.00 37.22 3.82
541 891 8.853077 ACAACTGAAGAAGATTAATGATCACA 57.147 30.769 0.00 0.00 37.22 3.58
542 892 9.552114 CAACAACTGAAGAAGATTAATGATCAC 57.448 33.333 0.00 0.00 37.22 3.06
543 893 9.506018 TCAACAACTGAAGAAGATTAATGATCA 57.494 29.630 0.00 0.00 37.22 2.92
544 894 9.766277 GTCAACAACTGAAGAAGATTAATGATC 57.234 33.333 0.00 0.00 35.22 2.92
545 895 9.288576 TGTCAACAACTGAAGAAGATTAATGAT 57.711 29.630 0.00 0.00 35.22 2.45
554 904 6.428385 AAGAACTGTCAACAACTGAAGAAG 57.572 37.500 0.00 0.00 35.22 2.85
639 997 9.144747 GAATGTGTGTATATAGCGAGATGAATT 57.855 33.333 0.00 0.00 0.00 2.17
655 1013 4.889995 TGAATTGGTTGGTGAATGTGTGTA 59.110 37.500 0.00 0.00 0.00 2.90
661 1019 2.924926 CGCATGAATTGGTTGGTGAATG 59.075 45.455 0.00 0.00 0.00 2.67
712 1071 1.757682 ACACGCTCTTTTTGTTCCCA 58.242 45.000 0.00 0.00 0.00 4.37
942 1496 1.743321 CTCTGGCCGGAGATGGAGAC 61.743 65.000 34.60 0.00 35.52 3.36
1013 1567 2.363038 CTCCTCTCCTCTTCTGATGCTG 59.637 54.545 0.00 0.00 0.00 4.41
1018 1578 1.638070 TGCTCTCCTCTCCTCTTCTGA 59.362 52.381 0.00 0.00 0.00 3.27
1019 1579 2.026641 CTGCTCTCCTCTCCTCTTCTG 58.973 57.143 0.00 0.00 0.00 3.02
1020 1580 1.922447 TCTGCTCTCCTCTCCTCTTCT 59.078 52.381 0.00 0.00 0.00 2.85
1021 1581 2.301346 CTCTGCTCTCCTCTCCTCTTC 58.699 57.143 0.00 0.00 0.00 2.87
1022 1582 1.063717 CCTCTGCTCTCCTCTCCTCTT 60.064 57.143 0.00 0.00 0.00 2.85
1023 1583 0.552848 CCTCTGCTCTCCTCTCCTCT 59.447 60.000 0.00 0.00 0.00 3.69
1024 1584 1.109323 GCCTCTGCTCTCCTCTCCTC 61.109 65.000 0.00 0.00 33.53 3.71
1025 1585 1.076044 GCCTCTGCTCTCCTCTCCT 60.076 63.158 0.00 0.00 33.53 3.69
1026 1586 2.489275 CGCCTCTGCTCTCCTCTCC 61.489 68.421 0.00 0.00 34.43 3.71
1027 1587 2.489275 CCGCCTCTGCTCTCCTCTC 61.489 68.421 0.00 0.00 34.43 3.20
1032 1592 1.752694 ACTCTCCGCCTCTGCTCTC 60.753 63.158 0.00 0.00 34.43 3.20
1046 1606 1.992557 ACACCTCTCTCTCCTCACTCT 59.007 52.381 0.00 0.00 0.00 3.24
1054 1614 1.305201 CTCCGCTACACCTCTCTCTC 58.695 60.000 0.00 0.00 0.00 3.20
1055 1615 0.106918 CCTCCGCTACACCTCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
1083 1643 4.394729 CACCTCCATCTCTCTCTACCTAC 58.605 52.174 0.00 0.00 0.00 3.18
1087 1647 1.960689 GCCACCTCCATCTCTCTCTAC 59.039 57.143 0.00 0.00 0.00 2.59
1088 1648 1.477740 CGCCACCTCCATCTCTCTCTA 60.478 57.143 0.00 0.00 0.00 2.43
1307 1870 4.530857 GATGGGCGTGGACTCCCG 62.531 72.222 0.43 0.00 43.80 5.14
1508 2074 4.227134 CTGACCCTGATCGGCCGG 62.227 72.222 27.83 10.66 0.00 6.13
1633 2199 0.179187 AGCAGAACTCGTCGTCGATG 60.179 55.000 8.20 8.20 45.21 3.84
2005 2571 0.177373 TCGACGAGGAGTAGCTGCTA 59.823 55.000 3.57 5.02 30.82 3.49
2142 2708 7.526142 AATAAAACTGTTCTCTTTCCTTCCC 57.474 36.000 0.00 0.00 0.00 3.97
2143 2709 7.041303 ACGAATAAAACTGTTCTCTTTCCTTCC 60.041 37.037 0.00 0.00 0.00 3.46
2320 2888 2.229784 CCAAGGAATTCAAGGTGTGCTC 59.770 50.000 7.93 0.00 0.00 4.26
2336 2904 0.462759 GTCGCCCAATCTCTCCAAGG 60.463 60.000 0.00 0.00 0.00 3.61
2339 2925 1.198094 TTGGTCGCCCAATCTCTCCA 61.198 55.000 0.00 0.00 45.93 3.86
2349 2965 4.966787 TGCAGGGTTTGGTCGCCC 62.967 66.667 0.00 0.00 45.16 6.13
2630 3254 3.190337 GGATTATTCCGTCCGTCCG 57.810 57.895 0.00 0.00 30.72 4.79
2733 3357 4.218200 GCTCATCTCATCTCAGCTAGCTAA 59.782 45.833 18.86 0.72 0.00 3.09
2735 3359 2.559668 GCTCATCTCATCTCAGCTAGCT 59.440 50.000 12.68 12.68 0.00 3.32
2736 3360 2.559668 AGCTCATCTCATCTCAGCTAGC 59.440 50.000 6.62 6.62 38.69 3.42
2737 3361 3.822167 TCAGCTCATCTCATCTCAGCTAG 59.178 47.826 0.00 0.00 38.40 3.42
2738 3362 3.822167 CTCAGCTCATCTCATCTCAGCTA 59.178 47.826 0.00 0.00 38.40 3.32
2739 3363 2.626266 CTCAGCTCATCTCATCTCAGCT 59.374 50.000 0.00 0.00 41.20 4.24
2740 3364 2.288579 CCTCAGCTCATCTCATCTCAGC 60.289 54.545 0.00 0.00 0.00 4.26
2741 3365 2.960384 ACCTCAGCTCATCTCATCTCAG 59.040 50.000 0.00 0.00 0.00 3.35
2742 3366 2.694109 CACCTCAGCTCATCTCATCTCA 59.306 50.000 0.00 0.00 0.00 3.27
2743 3367 2.694628 ACACCTCAGCTCATCTCATCTC 59.305 50.000 0.00 0.00 0.00 2.75
2782 3406 4.947645 AGTCTCTACGCTACCACTACTAG 58.052 47.826 0.00 0.00 0.00 2.57
2783 3407 5.114780 CAAGTCTCTACGCTACCACTACTA 58.885 45.833 0.00 0.00 0.00 1.82
2784 3408 3.910568 AGTCTCTACGCTACCACTACT 57.089 47.619 0.00 0.00 0.00 2.57
2785 3409 3.487209 GCAAGTCTCTACGCTACCACTAC 60.487 52.174 0.00 0.00 0.00 2.73
2786 3410 2.681848 GCAAGTCTCTACGCTACCACTA 59.318 50.000 0.00 0.00 0.00 2.74
2787 3411 1.473278 GCAAGTCTCTACGCTACCACT 59.527 52.381 0.00 0.00 0.00 4.00
2897 3521 4.060038 ACTACTCACAACTTGTCCAGTG 57.940 45.455 11.23 0.00 35.12 3.66
2901 3525 8.379457 AGAAAATTACTACTCACAACTTGTCC 57.621 34.615 0.00 0.00 0.00 4.02
2909 3533 5.248477 AGGCCAGAGAAAATTACTACTCACA 59.752 40.000 5.01 0.00 32.59 3.58
2947 3696 3.117512 ACAGTCCCAACCAAGACAATTCT 60.118 43.478 0.00 0.00 35.38 2.40
2972 3727 4.389077 AGCGTATCTTTCTTTCTTCCAACG 59.611 41.667 0.00 0.00 0.00 4.10
2976 3731 3.935828 AGCAGCGTATCTTTCTTTCTTCC 59.064 43.478 0.00 0.00 0.00 3.46
2977 3732 4.726306 GCAGCAGCGTATCTTTCTTTCTTC 60.726 45.833 0.00 0.00 0.00 2.87
2979 3734 2.675348 GCAGCAGCGTATCTTTCTTTCT 59.325 45.455 0.00 0.00 0.00 2.52
2980 3735 2.223135 GGCAGCAGCGTATCTTTCTTTC 60.223 50.000 0.00 0.00 43.41 2.62
2981 3736 1.740025 GGCAGCAGCGTATCTTTCTTT 59.260 47.619 0.00 0.00 43.41 2.52
3014 4007 1.448540 GATGGTGTCTGCTCCGGTG 60.449 63.158 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.