Multiple sequence alignment - TraesCS7B01G022400

Loading Multiple Alignment...

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 TraesCS7B01G022400 chr7B 100.000 3908 0 0 1 3908 21666002 21669909 0.000000e+00 7217.0
1 TraesCS7B01G022400 chr7B 88.197 610 44 12 2997 3600 21718791 21719378 0.000000e+00 702.0
2 TraesCS7B01G022400 chr7B 85.106 470 43 13 2620 3067 21815999 21816463 4.600000e-124 455.0
3 TraesCS7B01G022400 chr7B 82.731 498 67 12 3122 3605 21817717 21818209 3.610000e-115 425.0
4 TraesCS7B01G022400 chr7B 92.069 290 16 4 3604 3887 21719513 21719801 6.080000e-108 401.0
5 TraesCS7B01G022400 chr7D 88.495 2199 118 60 208 2333 75352191 75354327 0.000000e+00 2534.0
6 TraesCS7B01G022400 chr7D 84.915 1054 89 23 2609 3605 75355071 75356111 0.000000e+00 1002.0
7 TraesCS7B01G022400 chr7D 90.962 343 21 4 2267 2609 75354322 75354654 1.660000e-123 453.0
8 TraesCS7B01G022400 chr7D 84.000 375 36 6 13 364 75351748 75352121 4.840000e-89 339.0
9 TraesCS7B01G022400 chr7A 88.932 1825 101 34 827 2611 79640790 79642553 0.000000e+00 2158.0
10 TraesCS7B01G022400 chr7A 91.818 770 42 7 2609 3378 79642909 79643657 0.000000e+00 1053.0
11 TraesCS7B01G022400 chr7A 89.630 540 29 11 3374 3908 79643739 79644256 0.000000e+00 662.0
12 TraesCS7B01G022400 chr7A 89.602 327 25 3 3020 3346 79647534 79647851 1.310000e-109 407.0
13 TraesCS7B01G022400 chr7A 89.602 327 25 3 3020 3346 79651409 79651726 1.310000e-109 407.0
14 TraesCS7B01G022400 chr7A 85.538 325 11 13 443 732 79640127 79640450 1.360000e-79 307.0
15 TraesCS7B01G022400 chr7A 80.050 401 53 11 3 377 79639624 79640023 4.980000e-69 272.0
16 TraesCS7B01G022400 chr2A 93.182 44 0 2 1096 1139 768086295 768086335 1.170000e-05 62.1
17 TraesCS7B01G022400 chrUn 92.857 42 0 2 1096 1137 31689107 31689145 1.520000e-04 58.4
18 TraesCS7B01G022400 chr2D 92.857 42 0 2 1096 1137 643192433 643192471 1.520000e-04 58.4


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 TraesCS7B01G022400 chr7B 21666002 21669909 3907 False 7217.000000 7217 100.000000 1 3908 1 chr7B.!!$F1 3907
1 TraesCS7B01G022400 chr7B 21718791 21719801 1010 False 551.500000 702 90.133000 2997 3887 2 chr7B.!!$F2 890
2 TraesCS7B01G022400 chr7B 21815999 21818209 2210 False 440.000000 455 83.918500 2620 3605 2 chr7B.!!$F3 985
3 TraesCS7B01G022400 chr7D 75351748 75356111 4363 False 1082.000000 2534 87.093000 13 3605 4 chr7D.!!$F1 3592
4 TraesCS7B01G022400 chr7A 79639624 79651726 12102 False 752.285714 2158 87.881714 3 3908 7 chr7A.!!$F1 3905

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
401 666 0.035343 GGTAGAGTGTGGAAAGGGCC 60.035 60.0 0.00 0.0 0.0 5.80 F
408 673 0.183971 TGTGGAAAGGGCCTCGAAAA 59.816 50.0 6.46 0.0 0.0 2.29 F
1564 2136 0.543277 ATCTCATGCATCCACCGTGT 59.457 50.0 0.00 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2733 0.252239 AGGGGAGGGTTTGGAAATGC 60.252 55.0 0.00 0.0 0.00 3.56 R
2420 3087 5.447818 GGAGACATGAATTCCGAACATTGAC 60.448 44.0 0.00 0.0 0.00 3.18 R
2908 3991 0.250989 AGGAAAATGGTTCGCCGGAA 60.251 50.0 5.05 0.0 41.18 4.30 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
19 20 2.887889 CGTCGAGCCAAAACGCCAA 61.888 57.895 0.00 0.00 0.00 4.52
25 26 1.877443 GAGCCAAAACGCCAACTAAGA 59.123 47.619 0.00 0.00 0.00 2.10
32 33 5.391629 CCAAAACGCCAACTAAGAGATAACC 60.392 44.000 0.00 0.00 0.00 2.85
37 38 4.202264 CGCCAACTAAGAGATAACCTGGAT 60.202 45.833 0.00 0.00 0.00 3.41
50 51 3.652057 ACCTGGATCGACATGGAAATT 57.348 42.857 0.00 0.00 0.00 1.82
51 52 3.968265 ACCTGGATCGACATGGAAATTT 58.032 40.909 0.00 0.00 0.00 1.82
117 121 0.687354 GATCCCACCCGATACATGCT 59.313 55.000 0.00 0.00 0.00 3.79
151 155 2.125269 GCGCCACGAACCCTATGT 60.125 61.111 0.00 0.00 0.00 2.29
175 180 2.616969 GCTTCGTCAGCCAGAACAA 58.383 52.632 0.00 0.00 43.65 2.83
196 201 0.939106 TGCACCGATCGATGCATACG 60.939 55.000 32.84 7.64 46.63 3.06
229 249 0.250234 ATGGATGTGTGCACGCTAGT 59.750 50.000 29.04 16.10 0.00 2.57
235 255 1.864711 TGTGTGCACGCTAGTTCTTTC 59.135 47.619 29.04 0.00 0.00 2.62
236 256 1.864711 GTGTGCACGCTAGTTCTTTCA 59.135 47.619 22.93 0.00 0.00 2.69
237 257 1.864711 TGTGCACGCTAGTTCTTTCAC 59.135 47.619 13.13 0.00 0.00 3.18
241 261 1.382419 CACGCTAGTTCTTTCACGTCG 59.618 52.381 0.00 0.00 0.00 5.12
262 289 0.179100 CAACCTCTGCACCGATCGAT 60.179 55.000 18.66 0.00 0.00 3.59
263 290 0.179100 AACCTCTGCACCGATCGATG 60.179 55.000 18.66 11.93 0.00 3.84
280 308 3.119637 TCGATGCACACGACTTAAGATGA 60.120 43.478 10.09 0.00 34.85 2.92
290 318 1.459592 ACTTAAGATGAACGCGTGCAC 59.540 47.619 25.05 16.43 0.00 4.57
309 570 1.064783 GCTAGCCCTTTTGCATCGC 59.935 57.895 2.29 0.00 0.00 4.58
328 589 2.679716 GAGCCCCAACCTCTGCAT 59.320 61.111 0.00 0.00 0.00 3.96
357 618 2.671351 CGCACACGACTTAAGATGGACT 60.671 50.000 10.09 0.00 43.93 3.85
364 625 3.735208 CGACTTAAGATGGACTCGTGCAT 60.735 47.826 10.09 3.63 44.47 3.96
366 627 3.055819 ACTTAAGATGGACTCGTGCATGT 60.056 43.478 10.09 2.04 41.80 3.21
401 666 0.035343 GGTAGAGTGTGGAAAGGGCC 60.035 60.000 0.00 0.00 0.00 5.80
403 668 1.066071 GTAGAGTGTGGAAAGGGCCTC 60.066 57.143 6.46 0.00 0.00 4.70
405 670 1.827399 GAGTGTGGAAAGGGCCTCGA 61.827 60.000 6.46 0.00 0.00 4.04
408 673 0.183971 TGTGGAAAGGGCCTCGAAAA 59.816 50.000 6.46 0.00 0.00 2.29
580 873 0.908180 ACCACCACCTACCTACTGGC 60.908 60.000 0.00 0.00 36.63 4.85
582 875 1.342674 CCACCACCTACCTACTGGCTA 60.343 57.143 0.00 0.00 36.63 3.93
584 877 1.644864 ACCACCTACCTACTGGCTACT 59.355 52.381 0.00 0.00 36.63 2.57
585 878 2.032620 CCACCTACCTACTGGCTACTG 58.967 57.143 0.00 0.00 36.63 2.74
586 879 2.032620 CACCTACCTACTGGCTACTGG 58.967 57.143 0.00 0.00 36.63 4.00
903 1465 1.557443 CGCGGTCTGCTTCTCGTTTT 61.557 55.000 0.00 0.00 43.27 2.43
975 1537 1.153349 GTGGCAGGATTCCGGACTC 60.153 63.158 13.22 13.22 0.00 3.36
1462 2033 1.536073 CCTCCTGCTCTTCACCGTCA 61.536 60.000 0.00 0.00 0.00 4.35
1561 2133 1.957668 TTCATCTCATGCATCCACCG 58.042 50.000 0.00 0.00 0.00 4.94
1564 2136 0.543277 ATCTCATGCATCCACCGTGT 59.457 50.000 0.00 0.00 0.00 4.49
1580 2152 4.334481 CACCGTGTTTGTTTTACTTCCTCT 59.666 41.667 0.00 0.00 0.00 3.69
1726 2299 5.703730 TTAAATCTCCGGGTAGAATGGTT 57.296 39.130 0.00 0.00 0.00 3.67
1795 2369 5.408604 TCCATTCGAGCTTTGTTTTCTCTAC 59.591 40.000 0.00 0.00 0.00 2.59
1808 2398 8.754991 TTGTTTTCTCTACAATTGGTTCCTTA 57.245 30.769 10.83 0.00 30.96 2.69
1898 2492 0.601311 AGCACCGCTGACTGAAGAAC 60.601 55.000 0.00 0.00 37.57 3.01
1967 2575 2.877043 ACTTCGTTGGACGTTAGTGT 57.123 45.000 0.00 0.00 43.14 3.55
2120 2733 1.957089 CTTGTCGACTGTCTCACTCG 58.043 55.000 17.92 0.00 0.00 4.18
2133 2746 1.200020 CTCACTCGCATTTCCAAACCC 59.800 52.381 0.00 0.00 0.00 4.11
2284 2951 4.021916 TGTTCTACTACTAACCAGGAGCC 58.978 47.826 0.00 0.00 35.97 4.70
2286 2953 3.899726 TCTACTACTAACCAGGAGCCTG 58.100 50.000 9.59 9.59 35.97 4.85
2287 2954 2.625282 ACTACTAACCAGGAGCCTGT 57.375 50.000 14.97 0.67 42.15 4.00
2357 3024 2.359230 GAGGGCACAGACCACAGC 60.359 66.667 0.00 0.00 29.21 4.40
2396 3063 1.739562 CACGCTCAACTGCTCCCTC 60.740 63.158 0.00 0.00 0.00 4.30
2456 3123 3.462678 GTCTCCTCGGGCCCTGTC 61.463 72.222 22.43 0.00 0.00 3.51
2503 3170 1.076995 GGGTTGGACAGGTATGCCC 60.077 63.158 0.00 0.00 34.57 5.36
2507 3174 0.550914 TTGGACAGGTATGCCCATCC 59.449 55.000 11.80 11.80 38.92 3.51
2508 3175 0.623031 TGGACAGGTATGCCCATCCA 60.623 55.000 16.10 16.10 43.31 3.41
2509 3176 0.773644 GGACAGGTATGCCCATCCAT 59.226 55.000 13.35 0.00 38.53 3.41
2510 3177 1.271597 GGACAGGTATGCCCATCCATC 60.272 57.143 13.35 0.00 38.53 3.51
2511 3178 1.421268 GACAGGTATGCCCATCCATCA 59.579 52.381 0.00 0.00 34.66 3.07
2512 3179 1.422781 ACAGGTATGCCCATCCATCAG 59.577 52.381 0.00 0.00 34.66 2.90
2513 3180 0.403271 AGGTATGCCCATCCATCAGC 59.597 55.000 0.00 0.00 34.66 4.26
2514 3181 0.957395 GGTATGCCCATCCATCAGCG 60.957 60.000 0.00 0.00 0.00 5.18
2561 3228 1.190643 AACAGCCTAGAGAGAGGTGC 58.809 55.000 0.00 0.00 39.02 5.01
2562 3229 0.686112 ACAGCCTAGAGAGAGGTGCC 60.686 60.000 0.00 0.00 39.02 5.01
2570 3237 0.389166 GAGAGAGGTGCCTGTTGTCG 60.389 60.000 0.00 0.00 0.00 4.35
2605 3272 0.523072 CCTGGCAACTCATTTGTCCG 59.477 55.000 0.00 0.00 39.27 4.79
2611 3278 3.555518 GCAACTCATTTGTCCGTTTCTC 58.444 45.455 0.00 0.00 37.54 2.87
2612 3279 3.609409 GCAACTCATTTGTCCGTTTCTCC 60.609 47.826 0.00 0.00 37.54 3.71
2613 3280 3.771577 ACTCATTTGTCCGTTTCTCCT 57.228 42.857 0.00 0.00 0.00 3.69
2614 3281 4.884668 ACTCATTTGTCCGTTTCTCCTA 57.115 40.909 0.00 0.00 0.00 2.94
2615 3282 5.422214 ACTCATTTGTCCGTTTCTCCTAT 57.578 39.130 0.00 0.00 0.00 2.57
2616 3283 5.178797 ACTCATTTGTCCGTTTCTCCTATG 58.821 41.667 0.00 0.00 0.00 2.23
2621 3704 3.921677 TGTCCGTTTCTCCTATGTGAAC 58.078 45.455 0.00 0.00 0.00 3.18
2643 3726 3.326747 GCAGGTTCACAAGTACTACCAG 58.673 50.000 13.09 7.07 0.00 4.00
2843 3926 3.842126 CGTGTCGTGCCGCATCAG 61.842 66.667 0.00 0.00 0.00 2.90
2947 4052 2.294233 CTGTTCCTGCAGCTAAAAAGCA 59.706 45.455 8.66 0.00 37.25 3.91
2987 4092 7.584108 TGCTGAAGAACAATAAACATGTACTG 58.416 34.615 0.00 0.00 0.00 2.74
2989 4094 7.308589 GCTGAAGAACAATAAACATGTACTGGT 60.309 37.037 0.00 0.00 0.00 4.00
3050 4155 9.595823 TGTTTATATAAGTTACTCTCTTGTGCC 57.404 33.333 0.00 0.00 0.00 5.01
3055 4160 3.642778 TACTCTCTTGTGCCGCGGC 62.643 63.158 42.35 42.35 42.35 6.53
3072 4178 1.379527 GGCGGTTTTGTCTATGAGGG 58.620 55.000 0.00 0.00 0.00 4.30
3073 4179 1.065709 GGCGGTTTTGTCTATGAGGGA 60.066 52.381 0.00 0.00 0.00 4.20
3074 4180 2.421529 GGCGGTTTTGTCTATGAGGGAT 60.422 50.000 0.00 0.00 0.00 3.85
3075 4181 2.614057 GCGGTTTTGTCTATGAGGGATG 59.386 50.000 0.00 0.00 0.00 3.51
3076 4182 3.681594 GCGGTTTTGTCTATGAGGGATGA 60.682 47.826 0.00 0.00 0.00 2.92
3077 4183 4.122776 CGGTTTTGTCTATGAGGGATGAG 58.877 47.826 0.00 0.00 0.00 2.90
3078 4184 4.455606 GGTTTTGTCTATGAGGGATGAGG 58.544 47.826 0.00 0.00 0.00 3.86
3079 4185 3.845781 TTTGTCTATGAGGGATGAGGC 57.154 47.619 0.00 0.00 0.00 4.70
3173 5491 3.129638 ACTTCGCATCTAGGTTGAGAGAC 59.870 47.826 0.00 0.00 0.00 3.36
3192 5510 4.729868 AGACTAGGATTGGTTTTGTTGCT 58.270 39.130 0.00 0.00 0.00 3.91
3214 5536 6.375455 TGCTTCATATTTTCAGAGAAACTCCC 59.625 38.462 0.00 0.00 0.00 4.30
3215 5537 6.375455 GCTTCATATTTTCAGAGAAACTCCCA 59.625 38.462 0.00 0.00 0.00 4.37
3216 5538 7.067981 GCTTCATATTTTCAGAGAAACTCCCAT 59.932 37.037 0.00 0.00 0.00 4.00
3217 5539 8.884124 TTCATATTTTCAGAGAAACTCCCATT 57.116 30.769 0.00 0.00 0.00 3.16
3218 5540 8.284945 TCATATTTTCAGAGAAACTCCCATTG 57.715 34.615 0.00 0.00 0.00 2.82
3223 5545 7.889873 TTTCAGAGAAACTCCCATTGTTTTA 57.110 32.000 0.00 0.00 37.70 1.52
3268 5590 2.551071 GGTAGCTGGGGAGCAATATCAC 60.551 54.545 0.00 0.00 37.25 3.06
3269 5591 0.475906 AGCTGGGGAGCAATATCACC 59.524 55.000 0.00 0.00 43.67 4.02
3321 5643 2.947652 CGCATGACCTGAAGATGGATTT 59.052 45.455 0.00 0.00 0.00 2.17
3359 5681 6.126863 TCACTTGGAGAGGTTACATCATTT 57.873 37.500 0.00 0.00 0.00 2.32
3490 5945 1.869767 GATGATCGGACCAGCAATGTC 59.130 52.381 0.00 0.00 0.00 3.06
3498 5953 2.076100 GACCAGCAATGTCGTGATTGA 58.924 47.619 11.69 0.00 35.65 2.57
3504 5959 2.415759 GCAATGTCGTGATTGATTGCCA 60.416 45.455 11.69 0.00 43.15 4.92
3529 5984 0.379669 CGATCAAGATGCACCTTGGC 59.620 55.000 20.89 12.05 42.72 4.52
3533 5988 1.614903 TCAAGATGCACCTTGGCTTTG 59.385 47.619 20.89 0.00 42.72 2.77
3664 6252 2.203480 GGCACCAGCAGGGACAAA 60.203 61.111 0.00 0.00 44.61 2.83
3666 6254 2.270986 GCACCAGCAGGGACAAAGG 61.271 63.158 0.00 0.00 41.58 3.11
3667 6255 1.151450 CACCAGCAGGGACAAAGGT 59.849 57.895 0.00 0.00 41.15 3.50
3668 6256 0.890996 CACCAGCAGGGACAAAGGTC 60.891 60.000 0.00 0.00 43.55 3.85
3689 6279 2.112815 GGCGCACGGAGGCTAAAAT 61.113 57.895 10.83 0.00 0.00 1.82
3691 6281 0.248094 GCGCACGGAGGCTAAAATTC 60.248 55.000 0.30 0.00 0.00 2.17
3737 6328 8.847982 TCCCGATAAATAATCTGGATATACCA 57.152 34.615 0.00 0.00 41.57 3.25
3791 6382 6.961554 CCTTCTGTATCAAATTAAACGACAGC 59.038 38.462 0.00 0.00 34.25 4.40
3845 6436 4.282449 TGCAACTAAGTACAGCAGGAAGTA 59.718 41.667 0.00 0.00 0.00 2.24
3852 6443 5.091261 AGTACAGCAGGAAGTAAATCAGG 57.909 43.478 0.00 0.00 0.00 3.86
3889 6483 8.375506 AGATCAAATCAACACAAGGTTAGTAGA 58.624 33.333 0.00 0.00 37.72 2.59
3894 6488 5.607477 TCAACACAAGGTTAGTAGACTTGG 58.393 41.667 15.89 9.82 44.35 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.343421 GGCGTTTTGGCTCGACGT 61.343 61.111 0.00 0.00 40.72 4.34
1 2 2.887889 TTGGCGTTTTGGCTCGACG 61.888 57.895 0.00 0.00 45.14 5.12
19 20 5.446860 TGTCGATCCAGGTTATCTCTTAGT 58.553 41.667 0.00 0.00 0.00 2.24
25 26 3.576861 TCCATGTCGATCCAGGTTATCT 58.423 45.455 0.00 0.00 0.00 1.98
32 33 4.025396 CGAGAAATTTCCATGTCGATCCAG 60.025 45.833 17.84 0.00 0.00 3.86
37 38 5.120208 GTCTTTCGAGAAATTTCCATGTCGA 59.880 40.000 20.12 20.12 34.81 4.20
117 121 0.248094 CGCTTGCGTCGATGAGTCTA 60.248 55.000 9.31 0.00 0.00 2.59
134 138 2.125269 ACATAGGGTTCGTGGCGC 60.125 61.111 0.00 0.00 0.00 6.53
159 163 1.581934 CAGTTGTTCTGGCTGACGAA 58.418 50.000 0.00 0.00 40.23 3.85
170 175 1.061131 CATCGATCGGTGCAGTTGTTC 59.939 52.381 16.60 0.00 0.00 3.18
175 180 2.578664 TGCATCGATCGGTGCAGT 59.421 55.556 43.35 9.69 45.60 4.40
196 201 5.003804 ACACATCCATCTTAAGTTGTGTCC 58.996 41.667 17.05 0.00 42.81 4.02
229 249 0.179067 AGGTTGGCGACGTGAAAGAA 60.179 50.000 0.00 0.00 0.00 2.52
235 255 3.414700 GCAGAGGTTGGCGACGTG 61.415 66.667 4.52 0.64 0.00 4.49
236 256 3.923864 TGCAGAGGTTGGCGACGT 61.924 61.111 0.00 0.00 0.00 4.34
237 257 3.414700 GTGCAGAGGTTGGCGACG 61.415 66.667 0.00 0.00 0.00 5.12
241 261 2.045926 ATCGGTGCAGAGGTTGGC 60.046 61.111 0.00 0.00 0.00 4.52
262 289 2.729360 CGTTCATCTTAAGTCGTGTGCA 59.271 45.455 1.63 0.00 0.00 4.57
263 290 2.472397 GCGTTCATCTTAAGTCGTGTGC 60.472 50.000 1.63 0.00 0.00 4.57
290 318 1.353103 CGATGCAAAAGGGCTAGCG 59.647 57.895 9.00 0.00 34.04 4.26
297 325 2.100991 GCTCGGCGATGCAAAAGG 59.899 61.111 20.90 5.48 0.00 3.11
309 570 4.785453 GCAGAGGTTGGGGCTCGG 62.785 72.222 0.00 0.00 0.00 4.63
378 642 3.709587 CCCTTTCCACACTCTACCTCTA 58.290 50.000 0.00 0.00 0.00 2.43
379 643 2.541466 CCCTTTCCACACTCTACCTCT 58.459 52.381 0.00 0.00 0.00 3.69
380 644 1.066071 GCCCTTTCCACACTCTACCTC 60.066 57.143 0.00 0.00 0.00 3.85
384 648 1.276622 GAGGCCCTTTCCACACTCTA 58.723 55.000 0.00 0.00 0.00 2.43
387 652 1.415672 TTCGAGGCCCTTTCCACACT 61.416 55.000 0.00 0.00 0.00 3.55
415 687 0.178888 CCTCCCCTCTCCCCCTATTC 60.179 65.000 0.00 0.00 0.00 1.75
420 692 4.179599 CTCCCTCCCCTCTCCCCC 62.180 77.778 0.00 0.00 0.00 5.40
421 693 4.179599 CCTCCCTCCCCTCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
422 694 3.036959 TCCTCCCTCCCCTCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
425 697 1.864559 ACACTCCTCCCTCCCCTCT 60.865 63.158 0.00 0.00 0.00 3.69
551 828 0.321653 AGGTGGTGGTGAGATTTCGC 60.322 55.000 0.00 0.00 0.00 4.70
552 829 2.618053 GTAGGTGGTGGTGAGATTTCG 58.382 52.381 0.00 0.00 0.00 3.46
553 830 2.572104 AGGTAGGTGGTGGTGAGATTTC 59.428 50.000 0.00 0.00 0.00 2.17
559 845 1.551560 CCAGTAGGTAGGTGGTGGTGA 60.552 57.143 0.00 0.00 0.00 4.02
580 873 2.036992 GAGCAGGTGATGGATCCAGTAG 59.963 54.545 21.33 7.70 0.00 2.57
582 875 0.835941 GAGCAGGTGATGGATCCAGT 59.164 55.000 21.33 8.47 0.00 4.00
584 877 1.348008 GGGAGCAGGTGATGGATCCA 61.348 60.000 18.88 18.88 0.00 3.41
585 878 1.453669 GGGAGCAGGTGATGGATCC 59.546 63.158 4.20 4.20 0.00 3.36
586 879 1.453669 GGGGAGCAGGTGATGGATC 59.546 63.158 0.00 0.00 0.00 3.36
807 1129 2.130426 GCAGATGAGAGCTCCCGGA 61.130 63.158 10.93 0.00 0.00 5.14
809 1131 1.684386 AAGGCAGATGAGAGCTCCCG 61.684 60.000 10.93 0.00 0.00 5.14
810 1132 0.106521 GAAGGCAGATGAGAGCTCCC 59.893 60.000 10.93 0.00 0.00 4.30
820 1142 3.854669 CGGCGGGAGAAGGCAGAT 61.855 66.667 0.00 0.00 0.00 2.90
862 1418 3.503839 TGCGGGAGGGTTTTGGGT 61.504 61.111 0.00 0.00 0.00 4.51
903 1465 3.316868 ACCGAAAGAGCGAAAATGGAAAA 59.683 39.130 0.00 0.00 0.00 2.29
990 1552 3.853487 TGCATCATCTCCGCCGCT 61.853 61.111 0.00 0.00 0.00 5.52
1095 1657 4.808649 GGGCTCTGCACGTAGTAC 57.191 61.111 0.00 0.00 41.61 2.73
1462 2033 1.406065 CCCCAGACGATGAGGCAGAT 61.406 60.000 0.00 0.00 0.00 2.90
1523 2094 9.201989 GAGATGAATGGATATAGTATGGGTGTA 57.798 37.037 0.00 0.00 0.00 2.90
1533 2104 7.226918 GTGGATGCATGAGATGAATGGATATAG 59.773 40.741 2.46 0.00 36.36 1.31
1534 2105 7.052248 GTGGATGCATGAGATGAATGGATATA 58.948 38.462 2.46 0.00 36.36 0.86
1561 2133 5.034797 GTGCAGAGGAAGTAAAACAAACAC 58.965 41.667 0.00 0.00 0.00 3.32
1564 2136 4.947388 AGTGTGCAGAGGAAGTAAAACAAA 59.053 37.500 0.00 0.00 0.00 2.83
1580 2152 4.036734 GGAAAATTCAGTTCAGAGTGTGCA 59.963 41.667 0.00 0.00 0.00 4.57
1705 2278 5.221581 GCTAACCATTCTACCCGGAGATTTA 60.222 44.000 0.73 0.00 0.00 1.40
1726 2299 4.388485 TGCACAATTCAGAGTCTTTGCTA 58.612 39.130 3.43 0.00 0.00 3.49
1777 2351 5.853282 CCAATTGTAGAGAAAACAAAGCTCG 59.147 40.000 4.43 0.00 40.05 5.03
1795 2369 5.334105 CGTGTTCAGAGTAAGGAACCAATTG 60.334 44.000 0.00 0.00 42.04 2.32
1808 2398 3.815401 CCCTTTGATTTCGTGTTCAGAGT 59.185 43.478 0.00 0.00 0.00 3.24
1871 2465 2.256461 CAGCGGTGCTTTGCCTTC 59.744 61.111 0.00 0.00 36.40 3.46
1932 2540 5.494632 ACGAAGTTTGGTTTTTCGAAGAT 57.505 34.783 12.11 0.00 44.64 2.40
2120 2733 0.252239 AGGGGAGGGTTTGGAAATGC 60.252 55.000 0.00 0.00 0.00 3.56
2420 3087 5.447818 GGAGACATGAATTCCGAACATTGAC 60.448 44.000 0.00 0.00 0.00 3.18
2456 3123 1.006805 CTCCGAATAGAGCAGGCGG 60.007 63.158 0.00 0.00 43.11 6.13
2503 3170 1.227764 CAGGGGACGCTGATGGATG 60.228 63.158 10.50 0.00 0.00 3.51
2507 3174 4.864334 GGGCAGGGGACGCTGATG 62.864 72.222 18.98 3.77 0.00 3.07
2512 3179 4.678743 AAAAGGGGCAGGGGACGC 62.679 66.667 0.00 0.00 34.56 5.19
2513 3180 2.117423 AAAAAGGGGCAGGGGACG 59.883 61.111 0.00 0.00 0.00 4.79
2514 3181 1.913262 CCAAAAAGGGGCAGGGGAC 60.913 63.158 0.00 0.00 0.00 4.46
2561 3228 1.901650 GAAGAAGCGCCGACAACAGG 61.902 60.000 2.29 0.00 0.00 4.00
2562 3229 0.946221 AGAAGAAGCGCCGACAACAG 60.946 55.000 2.29 0.00 0.00 3.16
2570 3237 1.082690 CAGGAAGAAGAAGAAGCGCC 58.917 55.000 2.29 0.00 0.00 6.53
2572 3239 1.082690 GCCAGGAAGAAGAAGAAGCG 58.917 55.000 0.00 0.00 0.00 4.68
2605 3272 2.673368 CCTGCGTTCACATAGGAGAAAC 59.327 50.000 0.00 0.00 31.91 2.78
2621 3704 2.288579 TGGTAGTACTTGTGAACCTGCG 60.289 50.000 12.01 0.00 0.00 5.18
2908 3991 0.250989 AGGAAAATGGTTCGCCGGAA 60.251 50.000 5.05 0.00 41.18 4.30
3050 4155 1.060308 CATAGACAAAACCGCCGCG 59.940 57.895 5.59 5.59 0.00 6.46
3055 4160 4.122776 CTCATCCCTCATAGACAAAACCG 58.877 47.826 0.00 0.00 0.00 4.44
3072 4178 1.279271 AGGTACAACCACTGCCTCATC 59.721 52.381 0.00 0.00 41.95 2.92
3073 4179 1.362224 AGGTACAACCACTGCCTCAT 58.638 50.000 0.00 0.00 41.95 2.90
3074 4180 2.018355 TAGGTACAACCACTGCCTCA 57.982 50.000 0.00 0.00 41.95 3.86
3075 4181 2.236395 ACATAGGTACAACCACTGCCTC 59.764 50.000 0.00 0.00 41.95 4.70
3076 4182 2.027192 CACATAGGTACAACCACTGCCT 60.027 50.000 0.00 0.00 41.95 4.75
3077 4183 2.290071 ACACATAGGTACAACCACTGCC 60.290 50.000 0.00 0.00 41.95 4.85
3078 4184 2.742053 CACACATAGGTACAACCACTGC 59.258 50.000 0.00 0.00 41.95 4.40
3079 4185 3.244422 ACCACACATAGGTACAACCACTG 60.244 47.826 0.00 0.00 41.95 3.66
3173 5491 5.452078 TGAAGCAACAAAACCAATCCTAG 57.548 39.130 0.00 0.00 0.00 3.02
3192 5510 8.742777 CAATGGGAGTTTCTCTGAAAATATGAA 58.257 33.333 0.00 0.00 0.00 2.57
3214 5536 9.617975 GATCTCTTTTCTTCCTGTAAAACAATG 57.382 33.333 0.00 0.00 0.00 2.82
3215 5537 8.797438 GGATCTCTTTTCTTCCTGTAAAACAAT 58.203 33.333 0.00 0.00 0.00 2.71
3216 5538 7.777910 TGGATCTCTTTTCTTCCTGTAAAACAA 59.222 33.333 0.00 0.00 0.00 2.83
3217 5539 7.287061 TGGATCTCTTTTCTTCCTGTAAAACA 58.713 34.615 0.00 0.00 0.00 2.83
3218 5540 7.745620 TGGATCTCTTTTCTTCCTGTAAAAC 57.254 36.000 0.00 0.00 0.00 2.43
3223 5545 4.537688 TGGATGGATCTCTTTTCTTCCTGT 59.462 41.667 0.00 0.00 0.00 4.00
3268 5590 2.549064 TTGATCTATCCATGTGGCGG 57.451 50.000 0.00 0.00 34.44 6.13
3269 5591 3.405831 ACATTGATCTATCCATGTGGCG 58.594 45.455 8.44 0.00 40.40 5.69
3303 5625 4.264532 ACCCAAAATCCATCTTCAGGTCAT 60.265 41.667 0.00 0.00 0.00 3.06
3321 5643 0.399949 AGTGAGGTGACCAGACCCAA 60.400 55.000 3.63 0.00 36.56 4.12
3359 5681 1.757682 AGGCTCGAAAACAAACACCA 58.242 45.000 0.00 0.00 0.00 4.17
3490 5945 2.350102 CGGATGATGGCAATCAATCACG 60.350 50.000 8.12 6.76 45.81 4.35
3498 5953 3.497103 TCTTGATCGGATGATGGCAAT 57.503 42.857 0.00 0.00 34.09 3.56
3504 5959 2.371179 AGGTGCATCTTGATCGGATGAT 59.629 45.455 23.78 7.81 42.02 2.45
3529 5984 8.708742 TCAGAATGAATTCTACGTGTTACAAAG 58.291 33.333 7.05 0.00 45.97 2.77
3606 6192 2.036556 AAACAGATTTTGCAGCGTCG 57.963 45.000 0.00 0.00 0.00 5.12
3689 6279 8.483758 GGGATATTTACAGTAGAACTCTTGGAA 58.516 37.037 0.00 0.00 0.00 3.53
3691 6281 6.924060 CGGGATATTTACAGTAGAACTCTTGG 59.076 42.308 0.00 0.00 0.00 3.61
3729 6320 8.589338 TCTTTTTCAGAGCCTCTATGGTATATC 58.411 37.037 0.00 0.00 38.35 1.63
3737 6328 4.080129 TGCCATCTTTTTCAGAGCCTCTAT 60.080 41.667 0.00 0.00 33.87 1.98
3852 6443 9.195411 TGTGTTGATTTGATCTAGAAAAATTGC 57.805 29.630 14.59 10.11 0.00 3.56


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

AutoCloner maintained by Alex Coulton.