Multiple sequence alignment - TraesCS7B01G284500

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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 TraesCS7B01G284500 chr7B 100.000 3650 0 0 1 3650 518389823 518386174 0.000000e+00 6741.0
1 TraesCS7B01G284500 chr7D 91.365 2096 117 35 40 2105 489723048 489720987 0.000000e+00 2809.0
2 TraesCS7B01G284500 chr7D 95.672 1294 49 5 2357 3650 489720368 489719082 0.000000e+00 2073.0
3 TraesCS7B01G284500 chr7D 92.611 203 11 2 2112 2313 489720566 489720367 4.610000e-74 289.0
4 TraesCS7B01G284500 chr7A 86.445 2132 153 54 4 2081 556507415 556505366 0.000000e+00 2211.0
5 TraesCS7B01G284500 chr7A 86.431 877 61 27 2227 3062 556505357 556504498 0.000000e+00 907.0
6 TraesCS7B01G284500 chr7A 91.248 537 42 3 3117 3650 556504511 556503977 0.000000e+00 726.0
7 TraesCS7B01G284500 chr6B 88.785 214 24 0 1523 1736 223571472 223571259 2.800000e-66 263.0
8 TraesCS7B01G284500 chr6A 88.318 214 25 0 1523 1736 155224781 155224994 1.300000e-64 257.0
9 TraesCS7B01G284500 chr6D 87.383 214 27 0 1523 1736 125246960 125246747 2.810000e-61 246.0
10 TraesCS7B01G284500 chr5B 94.444 54 3 0 3068 3121 562467377 562467324 2.340000e-12 84.2
11 TraesCS7B01G284500 chr3B 92.727 55 3 1 3067 3121 202583412 202583359 1.090000e-10 78.7
12 TraesCS7B01G284500 chr3D 90.164 61 2 2 3065 3121 131807453 131807393 3.910000e-10 76.8


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 TraesCS7B01G284500 chr7B 518386174 518389823 3649 True 6741.000000 6741 100.000000 1 3650 1 chr7B.!!$R1 3649
1 TraesCS7B01G284500 chr7D 489719082 489723048 3966 True 1723.666667 2809 93.216000 40 3650 3 chr7D.!!$R1 3610
2 TraesCS7B01G284500 chr7A 556503977 556507415 3438 True 1281.333333 2211 88.041333 4 3650 3 chr7A.!!$R1 3646

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
38 39 0.034896 CGGGCTCTACCAACACTTGT 59.965 55.0 0.0 0.0 42.05 3.16 F
444 451 0.035458 ACCTCCGCTGGTTTCTTCTG 59.965 55.0 0.0 0.0 36.89 3.02 F
771 801 0.822811 TGAGAGAGTGAGAGCCATGC 59.177 55.0 0.0 0.0 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1208 1257 0.882042 AGCACACAAAGAGCGAGTGG 60.882 55.0 0.00 0.00 38.98 4.00 R
2437 2922 0.532417 GATTCCGCAGCTGCAGAGAT 60.532 55.0 36.03 24.11 42.21 2.75 R
2658 3144 1.220529 TGTTCTTCAGCTGTCGCTTG 58.779 50.0 14.67 0.00 46.47 4.01 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
24 25 3.374402 CTCACTGACGTCCGGGCT 61.374 66.667 14.12 0.00 0.00 5.19
26 27 3.374402 CACTGACGTCCGGGCTCT 61.374 66.667 14.12 0.00 0.00 4.09
30 31 2.753043 GACGTCCGGGCTCTACCA 60.753 66.667 3.66 0.00 42.05 3.25
31 32 2.283388 ACGTCCGGGCTCTACCAA 60.283 61.111 3.66 0.00 42.05 3.67
32 33 2.183555 CGTCCGGGCTCTACCAAC 59.816 66.667 3.66 0.00 42.05 3.77
33 34 2.642254 CGTCCGGGCTCTACCAACA 61.642 63.158 3.66 0.00 42.05 3.33
34 35 1.079336 GTCCGGGCTCTACCAACAC 60.079 63.158 0.00 0.00 42.05 3.32
35 36 1.229082 TCCGGGCTCTACCAACACT 60.229 57.895 0.00 0.00 42.05 3.55
36 37 0.834687 TCCGGGCTCTACCAACACTT 60.835 55.000 0.00 0.00 42.05 3.16
37 38 0.673644 CCGGGCTCTACCAACACTTG 60.674 60.000 0.00 0.00 42.05 3.16
38 39 0.034896 CGGGCTCTACCAACACTTGT 59.965 55.000 0.00 0.00 42.05 3.16
69 70 2.275380 GCCGCACCAAACCATCCTT 61.275 57.895 0.00 0.00 0.00 3.36
80 81 3.411517 CATCCTTGCCCGGTCCCT 61.412 66.667 0.00 0.00 0.00 4.20
142 143 1.727062 CACCCTCCTATCTCCTGCAT 58.273 55.000 0.00 0.00 0.00 3.96
193 194 1.144057 CCAGACCCGAAGAATCCCG 59.856 63.158 0.00 0.00 0.00 5.14
354 356 1.960689 GCTCTATCCACTCCCAGTCTC 59.039 57.143 0.00 0.00 0.00 3.36
383 385 0.669318 TGATTCCGCGTGGTGTTCTC 60.669 55.000 16.01 6.51 36.30 2.87
403 405 2.659610 GGCTGCTCTGTTCGTCCT 59.340 61.111 0.00 0.00 0.00 3.85
405 407 2.386660 GCTGCTCTGTTCGTCCTGC 61.387 63.158 0.00 0.00 0.00 4.85
433 440 2.668550 GCAACCGAAACCTCCGCT 60.669 61.111 0.00 0.00 0.00 5.52
443 450 2.453242 ACCTCCGCTGGTTTCTTCT 58.547 52.632 0.00 0.00 36.89 2.85
444 451 0.035458 ACCTCCGCTGGTTTCTTCTG 59.965 55.000 0.00 0.00 36.89 3.02
488 499 2.268022 GAGAACTCGACTGAGCCCA 58.732 57.895 0.00 0.00 46.69 5.36
514 537 2.350458 GCCCGGTCGGTACTTGGTA 61.350 63.158 8.67 0.00 0.00 3.25
536 559 2.438392 GGTAGGATTAGGTGGGGTCTTG 59.562 54.545 0.00 0.00 0.00 3.02
557 580 1.880941 CTTAGGTTAGCCCAGGGACT 58.119 55.000 10.89 8.78 43.88 3.85
616 645 1.721926 GTTGCTGTCAAGTACGCTCTC 59.278 52.381 0.00 0.00 31.93 3.20
628 657 1.439365 CGCTCTCGTTGTTTGCTGC 60.439 57.895 0.00 0.00 0.00 5.25
697 727 5.591643 TTTCAGATTCAGTCTTTGCGTAC 57.408 39.130 0.00 0.00 34.00 3.67
700 730 3.244181 AGATTCAGTCTTTGCGTACCGC 61.244 50.000 0.94 0.94 43.73 5.68
725 755 5.447010 GCTGTCTTGTGATTAGCTGATTGAC 60.447 44.000 0.00 0.00 34.55 3.18
734 764 8.206189 TGTGATTAGCTGATTGACTGATGATTA 58.794 33.333 0.00 0.00 0.00 1.75
735 765 8.494347 GTGATTAGCTGATTGACTGATGATTAC 58.506 37.037 0.00 0.00 0.00 1.89
744 774 5.438761 TGACTGATGATTACGACGATGAT 57.561 39.130 0.00 0.00 0.00 2.45
745 775 5.215160 TGACTGATGATTACGACGATGATG 58.785 41.667 0.00 0.00 0.00 3.07
746 776 5.008613 TGACTGATGATTACGACGATGATGA 59.991 40.000 0.00 0.00 0.00 2.92
748 778 6.273071 ACTGATGATTACGACGATGATGAAA 58.727 36.000 0.00 0.00 0.00 2.69
750 780 8.082242 ACTGATGATTACGACGATGATGAAATA 58.918 33.333 0.00 0.00 0.00 1.40
751 781 8.227731 TGATGATTACGACGATGATGAAATAC 57.772 34.615 0.00 0.00 0.00 1.89
752 782 8.082242 TGATGATTACGACGATGATGAAATACT 58.918 33.333 0.00 0.00 0.00 2.12
753 783 7.623268 TGATTACGACGATGATGAAATACTG 57.377 36.000 0.00 0.00 0.00 2.74
754 784 7.422399 TGATTACGACGATGATGAAATACTGA 58.578 34.615 0.00 0.00 0.00 3.41
755 785 7.591426 TGATTACGACGATGATGAAATACTGAG 59.409 37.037 0.00 0.00 0.00 3.35
756 786 5.500645 ACGACGATGATGAAATACTGAGA 57.499 39.130 0.00 0.00 0.00 3.27
768 798 3.660970 ATACTGAGAGAGTGAGAGCCA 57.339 47.619 0.00 0.00 35.96 4.75
771 801 0.822811 TGAGAGAGTGAGAGCCATGC 59.177 55.000 0.00 0.00 0.00 4.06
787 817 3.005554 CCATGCTCTTCTCGTGTGAAAT 58.994 45.455 0.00 0.00 0.00 2.17
795 825 6.237701 GCTCTTCTCGTGTGAAATAGAATGAC 60.238 42.308 0.00 0.00 0.00 3.06
797 827 6.586463 TCTTCTCGTGTGAAATAGAATGACAC 59.414 38.462 0.00 0.00 34.79 3.67
913 947 1.168714 GCAGGTACCAAAGCTTGAGG 58.831 55.000 15.94 14.84 32.16 3.86
917 951 2.303311 AGGTACCAAAGCTTGAGGTCTC 59.697 50.000 22.93 17.37 36.87 3.36
1036 1085 3.640407 GCCAGGACACCAGCAGGA 61.640 66.667 0.35 0.00 38.69 3.86
1208 1257 3.645268 AATTCGGTGAGCCCTGCCC 62.645 63.158 0.00 0.00 0.00 5.36
1247 1298 6.145535 GTGCTAGTCATTTTTCTTGTCCTTG 58.854 40.000 0.00 0.00 0.00 3.61
1255 1306 7.376072 GTCATTTTTCTTGTCCTTGTAAGTTCG 59.624 37.037 0.00 0.00 0.00 3.95
1259 1310 5.130292 TCTTGTCCTTGTAAGTTCGTAGG 57.870 43.478 0.00 0.00 0.00 3.18
1284 1335 3.741344 GCGAATTGCGATAGTGGTCTTAT 59.259 43.478 0.00 0.00 44.57 1.73
1302 1353 8.081633 TGGTCTTATTTGCTATGTTTTGAAGTG 58.918 33.333 0.00 0.00 0.00 3.16
1329 1381 3.648067 TGAAGGAGGAGCGGATCAATAAT 59.352 43.478 0.00 0.00 0.00 1.28
1420 1489 1.300971 TGCGGAAGAATGCTGCACTC 61.301 55.000 3.57 2.89 0.00 3.51
1509 1578 3.589988 ACTAACAGATCCAGAACTTGCG 58.410 45.455 0.00 0.00 0.00 4.85
1738 1807 4.505922 GTCAGAAGCAGTATCCTTCATTCG 59.494 45.833 4.24 0.00 40.83 3.34
1753 1822 7.156000 TCCTTCATTCGTTATACACTGTTTCA 58.844 34.615 0.00 0.00 0.00 2.69
1755 1824 7.095397 CCTTCATTCGTTATACACTGTTTCACA 60.095 37.037 0.00 0.00 0.00 3.58
1759 1828 9.689075 CATTCGTTATACACTGTTTCACATTAG 57.311 33.333 0.00 0.00 0.00 1.73
1767 1836 7.440523 ACACTGTTTCACATTAGAAGGAATC 57.559 36.000 0.00 0.00 0.00 2.52
1768 1837 6.998074 ACACTGTTTCACATTAGAAGGAATCA 59.002 34.615 0.00 0.00 0.00 2.57
1769 1838 7.667219 ACACTGTTTCACATTAGAAGGAATCAT 59.333 33.333 0.00 0.00 0.00 2.45
1770 1839 7.966753 CACTGTTTCACATTAGAAGGAATCATG 59.033 37.037 0.00 0.00 0.00 3.07
1771 1840 7.121759 ACTGTTTCACATTAGAAGGAATCATGG 59.878 37.037 0.00 0.00 0.00 3.66
1772 1841 6.127647 TGTTTCACATTAGAAGGAATCATGGC 60.128 38.462 0.00 0.00 0.00 4.40
1773 1842 5.378230 TCACATTAGAAGGAATCATGGCT 57.622 39.130 0.00 0.00 0.00 4.75
1827 1897 5.413833 AGATGGTATTCACAAACTTCTGCAG 59.586 40.000 7.63 7.63 0.00 4.41
1831 1901 5.182001 GGTATTCACAAACTTCTGCAGTCAT 59.818 40.000 14.67 0.00 32.94 3.06
1839 1909 3.406764 ACTTCTGCAGTCATTTCCTGTC 58.593 45.455 14.67 0.00 32.41 3.51
1861 1931 7.978982 TGTCTTAGGTCTCGTACACTAATTAC 58.021 38.462 0.00 0.00 0.00 1.89
1875 1945 5.640783 ACACTAATTACGCAGGAGTTTTACC 59.359 40.000 0.00 0.00 0.00 2.85
2075 2145 6.183360 CCGTATAGCCATGAAAAGATTTGGTT 60.183 38.462 0.00 0.00 0.00 3.67
2099 2169 9.021863 GTTAGTTCACATACTTCATAGTAGCAC 57.978 37.037 0.00 0.00 40.09 4.40
2102 2172 3.736252 CACATACTTCATAGTAGCACGCC 59.264 47.826 0.00 0.00 40.09 5.68
2158 2642 8.792633 CACATCTTTTTCTCATACCAAAGGTAA 58.207 33.333 0.00 0.00 41.85 2.85
2224 2708 4.672587 TTGACTGGACATATGCCTACTC 57.327 45.455 14.63 8.50 0.00 2.59
2265 2749 3.660501 AATCTCCGTTTGCCCTTTTTC 57.339 42.857 0.00 0.00 0.00 2.29
2270 2755 3.558033 TCCGTTTGCCCTTTTTCTTACT 58.442 40.909 0.00 0.00 0.00 2.24
2292 2777 5.536538 ACTTTCACTCTACACTCATGAGTCA 59.463 40.000 25.58 14.95 40.20 3.41
2328 2813 8.514594 TGAAGAAAACTAAATATGCACAGGAAG 58.485 33.333 0.00 0.00 0.00 3.46
2343 2828 1.350351 AGGAAGATGCTTGACACTGCT 59.650 47.619 0.00 0.00 0.00 4.24
2344 2829 2.568956 AGGAAGATGCTTGACACTGCTA 59.431 45.455 0.00 0.00 0.00 3.49
2345 2830 2.675348 GGAAGATGCTTGACACTGCTAC 59.325 50.000 0.00 0.00 0.00 3.58
2346 2831 2.393271 AGATGCTTGACACTGCTACC 57.607 50.000 1.99 0.00 0.00 3.18
2347 2832 1.625315 AGATGCTTGACACTGCTACCA 59.375 47.619 1.99 0.00 0.00 3.25
2348 2833 2.005451 GATGCTTGACACTGCTACCAG 58.995 52.381 1.99 0.00 44.80 4.00
2387 2872 6.999950 TGTAGCTACTTGATGTCACCTTTTA 58.000 36.000 23.84 0.00 0.00 1.52
2404 2889 5.413833 ACCTTTTAACAGCATCATCTGTGAG 59.586 40.000 0.00 0.00 45.77 3.51
2437 2922 3.808726 GCTTCATTGTGAATGTTTTGCCA 59.191 39.130 0.00 0.00 39.87 4.92
2491 2976 4.082845 TCTGCACTGTTAGTCTAGAAGCT 58.917 43.478 0.00 0.00 0.00 3.74
2658 3144 2.595188 CGACGATGAATGAACGATGTGC 60.595 50.000 0.00 0.00 0.00 4.57
2720 3208 5.782047 TGCATGGTGGTTTTATCTTCTTTG 58.218 37.500 0.00 0.00 0.00 2.77
2807 3311 4.567959 GCCTCCATTGCACAAATTATGTTC 59.432 41.667 0.00 0.00 41.46 3.18
2930 3455 6.710744 AGATTGTGAAATCAGTTTAACGACCT 59.289 34.615 0.00 0.00 32.20 3.85
2957 3482 2.412325 CGAGCCCAAAATCACGTACAAC 60.412 50.000 0.00 0.00 0.00 3.32
2984 3509 2.668279 GCCCAATAACAGCAGTTTCACG 60.668 50.000 0.00 0.00 39.15 4.35
2993 3518 3.814842 ACAGCAGTTTCACGATGATGAAA 59.185 39.130 0.00 0.00 44.40 2.69
3018 3543 3.553511 GCTCCAGATCGTTAACATCACAG 59.446 47.826 6.39 6.51 0.00 3.66
3063 3588 7.550906 AGCCTCTGATAGAATAAACACAAGTTC 59.449 37.037 0.00 0.00 36.84 3.01
3065 3590 9.442047 CCTCTGATAGAATAAACACAAGTTCTT 57.558 33.333 0.00 0.00 36.84 2.52
3209 3734 4.726583 ACCAATAGCTCTACCGACTGATA 58.273 43.478 0.00 0.00 0.00 2.15
3229 3754 1.683917 AGATACAGCTAGCGAACCCTG 59.316 52.381 9.55 3.28 0.00 4.45
3416 3944 2.647297 GCCAAGGCTGTTGCTGAC 59.353 61.111 3.29 0.00 39.59 3.51
3529 4057 3.122613 GCAGTCGTCATGTGAAGAAAGAG 59.877 47.826 0.28 0.00 34.54 2.85
3579 4107 2.591429 CCACTTGCAGTCACGGCA 60.591 61.111 0.00 0.00 40.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.529214 CGGACGTCAGTGAGTGATACG 60.529 57.143 18.91 2.90 37.56 3.06
1 2 1.202154 CCGGACGTCAGTGAGTGATAC 60.202 57.143 18.91 0.00 37.56 2.24
2 3 1.092348 CCGGACGTCAGTGAGTGATA 58.908 55.000 18.91 0.00 37.56 2.15
10 11 2.045131 GTAGAGCCCGGACGTCAGT 61.045 63.158 18.91 0.00 0.00 3.41
24 25 1.418637 GTGGGGACAAGTGTTGGTAGA 59.581 52.381 0.00 0.00 46.06 2.59
26 27 1.214217 TGTGGGGACAAGTGTTGGTA 58.786 50.000 0.00 0.00 46.06 3.25
30 31 1.214175 TGACATGTGGGGACAAGTGTT 59.786 47.619 1.15 0.00 46.06 3.32
31 32 0.843309 TGACATGTGGGGACAAGTGT 59.157 50.000 1.15 0.00 46.06 3.55
32 33 1.527034 CTGACATGTGGGGACAAGTG 58.473 55.000 1.15 0.00 46.06 3.16
33 34 0.250901 GCTGACATGTGGGGACAAGT 60.251 55.000 1.15 0.00 46.06 3.16
34 35 0.962356 GGCTGACATGTGGGGACAAG 60.962 60.000 1.15 0.00 46.06 3.16
35 36 1.074775 GGCTGACATGTGGGGACAA 59.925 57.895 1.15 0.00 46.06 3.18
36 37 2.756400 GGCTGACATGTGGGGACA 59.244 61.111 1.15 0.00 38.70 4.02
37 38 2.436646 CGGCTGACATGTGGGGAC 60.437 66.667 1.15 0.00 0.00 4.46
38 39 4.408821 GCGGCTGACATGTGGGGA 62.409 66.667 1.15 0.00 0.00 4.81
118 119 1.465200 GGAGATAGGAGGGTGGCGAC 61.465 65.000 0.00 0.00 0.00 5.19
119 120 1.152525 GGAGATAGGAGGGTGGCGA 60.153 63.158 0.00 0.00 0.00 5.54
121 122 1.763546 GCAGGAGATAGGAGGGTGGC 61.764 65.000 0.00 0.00 0.00 5.01
122 123 0.399091 TGCAGGAGATAGGAGGGTGG 60.399 60.000 0.00 0.00 0.00 4.61
123 124 1.622811 GATGCAGGAGATAGGAGGGTG 59.377 57.143 0.00 0.00 0.00 4.61
124 125 1.825242 CGATGCAGGAGATAGGAGGGT 60.825 57.143 0.00 0.00 0.00 4.34
125 126 0.894141 CGATGCAGGAGATAGGAGGG 59.106 60.000 0.00 0.00 0.00 4.30
142 143 3.146847 GAGGGAAGCTTTTCCTTTTCGA 58.853 45.455 19.19 0.00 40.90 3.71
193 194 1.557099 ATTTTTCCTTCTTCGCCCCC 58.443 50.000 0.00 0.00 0.00 5.40
234 235 1.153549 GGAAGGCACGAGCTTCGAT 60.154 57.895 4.48 0.00 43.74 3.59
409 411 3.091022 GTTTCGGTTGCTTGCGCG 61.091 61.111 0.00 0.00 39.65 6.86
427 434 0.674895 CCCAGAAGAAACCAGCGGAG 60.675 60.000 1.50 0.00 0.00 4.63
433 440 2.600790 TCGTCTACCCAGAAGAAACCA 58.399 47.619 0.00 0.00 36.51 3.67
442 449 2.213499 GCCAAATCATCGTCTACCCAG 58.787 52.381 0.00 0.00 0.00 4.45
443 450 1.472552 CGCCAAATCATCGTCTACCCA 60.473 52.381 0.00 0.00 0.00 4.51
444 451 1.217882 CGCCAAATCATCGTCTACCC 58.782 55.000 0.00 0.00 0.00 3.69
478 489 1.216710 CTCGGTCTTGGGCTCAGTC 59.783 63.158 0.00 0.00 0.00 3.51
503 526 4.522022 CCTAATCCTACCTACCAAGTACCG 59.478 50.000 0.00 0.00 0.00 4.02
514 537 1.945317 AGACCCCACCTAATCCTACCT 59.055 52.381 0.00 0.00 0.00 3.08
557 580 3.439857 AAGAATCTAGGCACAGGCAAA 57.560 42.857 0.00 0.00 43.71 3.68
593 616 2.480419 GAGCGTACTTGACAGCAACAAT 59.520 45.455 0.00 0.00 32.26 2.71
595 618 1.068588 AGAGCGTACTTGACAGCAACA 59.931 47.619 0.00 0.00 32.26 3.33
596 619 1.721926 GAGAGCGTACTTGACAGCAAC 59.278 52.381 0.00 0.00 32.26 4.17
648 677 0.674581 TGAGGAAATCTGCAGTGGCG 60.675 55.000 14.67 0.00 45.35 5.69
657 686 6.537355 TCTGAAATGAACAGTGAGGAAATCT 58.463 36.000 0.00 0.00 36.81 2.40
697 727 0.647410 CTAATCACAAGACAGCGCGG 59.353 55.000 8.83 5.83 0.00 6.46
700 730 2.610433 TCAGCTAATCACAAGACAGCG 58.390 47.619 0.00 0.00 39.16 5.18
703 733 5.640783 CAGTCAATCAGCTAATCACAAGACA 59.359 40.000 0.00 0.00 0.00 3.41
725 755 6.753897 TTTCATCATCGTCGTAATCATCAG 57.246 37.500 0.00 0.00 0.00 2.90
734 764 5.297029 TCTCTCAGTATTTCATCATCGTCGT 59.703 40.000 0.00 0.00 0.00 4.34
735 765 5.752712 TCTCTCAGTATTTCATCATCGTCG 58.247 41.667 0.00 0.00 0.00 5.12
744 774 4.400884 GGCTCTCACTCTCTCAGTATTTCA 59.599 45.833 0.00 0.00 32.21 2.69
745 775 4.400884 TGGCTCTCACTCTCTCAGTATTTC 59.599 45.833 0.00 0.00 32.21 2.17
746 776 4.348486 TGGCTCTCACTCTCTCAGTATTT 58.652 43.478 0.00 0.00 32.21 1.40
748 778 3.660970 TGGCTCTCACTCTCTCAGTAT 57.339 47.619 0.00 0.00 32.21 2.12
750 780 2.101783 CATGGCTCTCACTCTCTCAGT 58.898 52.381 0.00 0.00 34.67 3.41
751 781 1.202440 GCATGGCTCTCACTCTCTCAG 60.202 57.143 0.00 0.00 0.00 3.35
752 782 0.822811 GCATGGCTCTCACTCTCTCA 59.177 55.000 0.00 0.00 0.00 3.27
753 783 1.113788 AGCATGGCTCTCACTCTCTC 58.886 55.000 0.00 0.00 30.62 3.20
754 784 3.303462 AGCATGGCTCTCACTCTCT 57.697 52.632 0.00 0.00 30.62 3.10
768 798 5.330455 TCTATTTCACACGAGAAGAGCAT 57.670 39.130 0.00 0.00 0.00 3.79
771 801 6.808704 TGTCATTCTATTTCACACGAGAAGAG 59.191 38.462 0.00 0.00 31.76 2.85
810 840 2.352127 CGCATTCAGAGTCACTCAGTCA 60.352 50.000 7.77 0.00 32.06 3.41
811 841 2.257894 CGCATTCAGAGTCACTCAGTC 58.742 52.381 7.77 0.00 32.06 3.51
812 842 1.067283 CCGCATTCAGAGTCACTCAGT 60.067 52.381 7.77 0.00 32.06 3.41
813 843 1.067283 ACCGCATTCAGAGTCACTCAG 60.067 52.381 7.77 0.00 32.06 3.35
814 844 0.969149 ACCGCATTCAGAGTCACTCA 59.031 50.000 7.77 0.00 32.06 3.41
815 845 2.803451 CTACCGCATTCAGAGTCACTC 58.197 52.381 0.00 0.00 0.00 3.51
816 846 1.134965 GCTACCGCATTCAGAGTCACT 60.135 52.381 0.00 0.00 35.78 3.41
817 847 1.134965 AGCTACCGCATTCAGAGTCAC 60.135 52.381 0.00 0.00 39.10 3.67
898 932 3.402628 TGAGACCTCAAGCTTTGGTAC 57.597 47.619 17.88 15.20 36.53 3.34
913 947 5.105554 ACCATAGTTGTCTGTCAGATGAGAC 60.106 44.000 5.68 3.22 39.31 3.36
917 951 5.482006 TGAACCATAGTTGTCTGTCAGATG 58.518 41.667 5.68 0.00 35.94 2.90
1036 1085 4.889112 CATGCCATGCGAGCCCCT 62.889 66.667 0.00 0.00 0.00 4.79
1146 1195 2.076863 CTCAAGCCCTCGTCGATTTTT 58.923 47.619 0.00 0.00 0.00 1.94
1208 1257 0.882042 AGCACACAAAGAGCGAGTGG 60.882 55.000 0.00 0.00 38.98 4.00
1255 1306 3.669122 CACTATCGCAATTCGCTACCTAC 59.331 47.826 0.00 0.00 39.08 3.18
1259 1310 2.470821 ACCACTATCGCAATTCGCTAC 58.529 47.619 0.00 0.00 39.08 3.58
1270 1321 7.715265 AACATAGCAAATAAGACCACTATCG 57.285 36.000 0.00 0.00 0.00 2.92
1273 1324 8.856153 TCAAAACATAGCAAATAAGACCACTA 57.144 30.769 0.00 0.00 0.00 2.74
1278 1329 9.846248 ATCACTTCAAAACATAGCAAATAAGAC 57.154 29.630 0.00 0.00 0.00 3.01
1302 1353 3.259374 TGATCCGCTCCTCCTTCATTATC 59.741 47.826 0.00 0.00 0.00 1.75
1364 1433 6.129393 CACTGTAAAACATCACTTGAACTCG 58.871 40.000 0.00 0.00 0.00 4.18
1397 1466 1.134431 TGCAGCATTCTTCCGCATAGA 60.134 47.619 0.00 0.00 0.00 1.98
1420 1489 6.021596 GCACAAGTCGGTTAATATTTGTCAG 58.978 40.000 0.00 0.00 0.00 3.51
1476 1545 7.444183 TCTGGATCTGTTAGTTACACAAAAAGG 59.556 37.037 0.00 0.00 32.10 3.11
1509 1578 5.923733 TCTTCATCTGAGAAAGGTAGGAC 57.076 43.478 0.00 0.00 0.00 3.85
1753 1822 8.773033 ATTTAAGCCATGATTCCTTCTAATGT 57.227 30.769 0.00 0.00 0.00 2.71
1759 1828 9.635520 CAATCATATTTAAGCCATGATTCCTTC 57.364 33.333 13.87 0.00 43.91 3.46
1839 1909 5.906285 GCGTAATTAGTGTACGAGACCTAAG 59.094 44.000 8.08 0.00 45.63 2.18
1861 1931 3.081804 AGGAAATGGTAAAACTCCTGCG 58.918 45.455 0.00 0.00 35.16 5.18
1875 1945 8.405531 TCTTCTGTGTTTTCAGTTAAGGAAATG 58.594 33.333 3.76 0.00 34.50 2.32
1981 2051 4.878968 TCTCATCCTTACTCACATACCCA 58.121 43.478 0.00 0.00 0.00 4.51
2075 2145 7.415229 CGTGCTACTATGAAGTATGTGAACTA 58.585 38.462 0.00 0.00 37.57 2.24
2132 2616 7.219484 ACCTTTGGTATGAGAAAAAGATGTG 57.781 36.000 0.00 0.00 32.11 3.21
2170 2654 6.698008 TTCATTTGAAGAGACATTGTGTGT 57.302 33.333 0.00 0.00 45.83 3.72
2251 2735 5.231357 GTGAAAGTAAGAAAAAGGGCAAACG 59.769 40.000 0.00 0.00 0.00 3.60
2265 2749 7.598278 ACTCATGAGTGTAGAGTGAAAGTAAG 58.402 38.462 27.37 0.00 40.83 2.34
2270 2755 6.209391 TGATGACTCATGAGTGTAGAGTGAAA 59.791 38.462 32.50 4.55 42.29 2.69
2328 2813 2.005451 CTGGTAGCAGTGTCAAGCATC 58.995 52.381 13.89 0.00 0.00 3.91
2343 2828 3.104512 CATTCAGAGGGTGGTACTGGTA 58.895 50.000 0.00 0.00 33.19 3.25
2344 2829 1.909302 CATTCAGAGGGTGGTACTGGT 59.091 52.381 0.00 0.00 33.19 4.00
2345 2830 1.909302 ACATTCAGAGGGTGGTACTGG 59.091 52.381 0.00 0.00 33.19 4.00
2346 2831 3.430929 GCTACATTCAGAGGGTGGTACTG 60.431 52.174 0.00 0.00 0.00 2.74
2347 2832 2.766828 GCTACATTCAGAGGGTGGTACT 59.233 50.000 0.00 0.00 0.00 2.73
2348 2833 2.766828 AGCTACATTCAGAGGGTGGTAC 59.233 50.000 0.00 0.00 0.00 3.34
2349 2834 3.116096 AGCTACATTCAGAGGGTGGTA 57.884 47.619 0.00 0.00 0.00 3.25
2353 2838 4.353777 TCAAGTAGCTACATTCAGAGGGT 58.646 43.478 25.28 0.00 0.00 4.34
2387 2872 2.484742 TGCTCACAGATGATGCTGTT 57.515 45.000 0.00 0.00 46.42 3.16
2404 2889 3.251729 TCACAATGAAGCAGAGAGTTTGC 59.748 43.478 0.00 0.00 41.83 3.68
2437 2922 0.532417 GATTCCGCAGCTGCAGAGAT 60.532 55.000 36.03 24.11 42.21 2.75
2491 2976 7.985184 ACATTAGTTACCGAATAAGAAGATGCA 59.015 33.333 0.00 0.00 0.00 3.96
2658 3144 1.220529 TGTTCTTCAGCTGTCGCTTG 58.779 50.000 14.67 0.00 46.47 4.01
2675 3161 5.163519 GCAACCAATTTATAGTCAGCCATGT 60.164 40.000 0.00 0.00 0.00 3.21
2676 3162 5.163530 TGCAACCAATTTATAGTCAGCCATG 60.164 40.000 0.00 0.00 0.00 3.66
2720 3208 7.987268 TGTCAGTCATTCTATTACGAACATC 57.013 36.000 0.00 0.00 0.00 3.06
2807 3311 3.362693 GCGGTCTCTTTTGTTTACGACAG 60.363 47.826 0.00 0.00 39.94 3.51
2930 3455 2.639065 GTGATTTTGGGCTCGGTATCA 58.361 47.619 0.00 0.00 0.00 2.15
2957 3482 0.679640 TGCTGTTATTGGGCTTCGGG 60.680 55.000 0.00 0.00 0.00 5.14
2984 3509 4.574013 ACGATCTGGAGCTTTTTCATCATC 59.426 41.667 0.00 0.00 0.00 2.92
2993 3518 4.631813 GTGATGTTAACGATCTGGAGCTTT 59.368 41.667 14.81 0.00 0.00 3.51
3018 3543 4.884164 AGGCTCCATGCTATTTTAACAGAC 59.116 41.667 0.00 0.00 42.39 3.51
3074 3599 7.395772 TGGATCAATAAAGTGTTGGCAAATCTA 59.604 33.333 0.00 0.00 0.00 1.98
3147 3672 2.022764 TGTGTACCATGCCTTCGATG 57.977 50.000 0.00 0.00 0.00 3.84
3162 3687 8.194104 GTCAATAGAACAGAGTAGATGATGTGT 58.806 37.037 0.00 0.00 0.00 3.72
3209 3734 1.683917 CAGGGTTCGCTAGCTGTATCT 59.316 52.381 13.93 2.16 0.00 1.98
3229 3754 2.561569 CCCGGGTAGTGATGTTTGATC 58.438 52.381 14.18 0.00 0.00 2.92
3416 3944 0.749649 AGATAGCAAGAGGGCTCGTG 59.250 55.000 0.00 0.00 44.54 4.35
3529 4057 2.395651 CAGATGAGCTGCTCAAGGC 58.604 57.895 33.31 24.27 44.04 4.35


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

AutoCloner maintained by Alex Coulton.