Multiple sequence alignment - TraesCS7B01G333200

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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 TraesCS7B01G333200 chr7B 100.000 2161 0 0 1914 4074 588383529 588381369 0.000000e+00 3991.0
1 TraesCS7B01G333200 chr7B 100.000 1451 0 0 1 1451 588385442 588383992 0.000000e+00 2680.0
2 TraesCS7B01G333200 chr7B 81.034 116 18 4 2284 2397 483533501 483533614 5.610000e-14 89.8
3 TraesCS7B01G333200 chr7D 87.624 1406 75 47 1932 3277 544998319 544996953 0.000000e+00 1541.0
4 TraesCS7B01G333200 chr7D 90.879 603 25 10 3299 3891 544996860 544996278 0.000000e+00 782.0
5 TraesCS7B01G333200 chr7D 88.095 672 41 25 793 1449 544999044 544998397 0.000000e+00 761.0
6 TraesCS7B01G333200 chr7D 82.236 653 45 46 128 723 545000002 544999364 7.860000e-137 497.0
7 TraesCS7B01G333200 chr7D 88.995 209 9 2 3880 4074 544996257 544996049 3.150000e-61 246.0
8 TraesCS7B01G333200 chr7D 81.034 116 18 4 2284 2397 461091957 461092070 5.610000e-14 89.8
9 TraesCS7B01G333200 chr7D 90.141 71 3 2 291 358 545176261 545176192 5.610000e-14 89.8
10 TraesCS7B01G333200 chr7A 94.207 794 27 11 1929 2711 626885564 626884779 0.000000e+00 1194.0
11 TraesCS7B01G333200 chr7A 88.388 999 42 29 498 1451 626886623 626885654 0.000000e+00 1134.0
12 TraesCS7B01G333200 chr7A 88.205 780 37 20 3310 4074 626884238 626883499 0.000000e+00 880.0
13 TraesCS7B01G333200 chr7A 87.844 436 28 6 2852 3283 626884743 626884329 4.730000e-134 488.0
14 TraesCS7B01G333200 chr7A 80.620 129 24 1 1993 2121 465377046 465377173 9.320000e-17 99.0
15 TraesCS7B01G333200 chr2A 82.996 247 38 4 1207 1451 733518664 733518420 1.910000e-53 220.0
16 TraesCS7B01G333200 chr2A 89.928 139 14 0 2284 2422 733517886 733517748 3.240000e-41 180.0
17 TraesCS7B01G333200 chr2A 75.988 329 56 16 1972 2286 733518316 733517997 9.120000e-32 148.0
18 TraesCS7B01G333200 chr2D 82.787 244 40 2 1207 1449 599791072 599790830 2.470000e-52 217.0
19 TraesCS7B01G333200 chr2D 92.806 139 10 0 2284 2422 599790258 599790120 6.900000e-48 202.0
20 TraesCS7B01G333200 chr2D 84.106 151 22 2 1972 2121 599790732 599790583 1.180000e-30 145.0
21 TraesCS7B01G333200 chr2B 91.367 139 12 0 2284 2422 729135555 729135417 1.490000e-44 191.0
22 TraesCS7B01G333200 chr2B 77.370 327 51 15 1972 2286 729136012 729135697 5.410000e-39 172.0
23 TraesCS7B01G333200 chr6B 100.000 55 0 0 3935 3989 712054395 712054341 7.200000e-18 102.0


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 TraesCS7B01G333200 chr7B 588381369 588385442 4073 True 3335.5 3991 100.0000 1 4074 2 chr7B.!!$R1 4073
1 TraesCS7B01G333200 chr7D 544996049 545000002 3953 True 765.4 1541 87.5658 128 4074 5 chr7D.!!$R2 3946
2 TraesCS7B01G333200 chr7A 626883499 626886623 3124 True 924.0 1194 89.6610 498 4074 4 chr7A.!!$R1 3576

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
821 1182 0.109412 GGCGTTACGTAGCACTCTGT 60.109 55.0 10.16 0.0 34.54 3.41 F
2133 2543 0.034059 CCCAGGTCAGTCACTCACAC 59.966 60.0 0.00 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2769 3204 0.099613 CGTCGAGACATGTGCTAGCT 59.900 55.0 17.23 0.0 0.0 3.32 R
3092 3553 0.441533 GCAAGCATCACACTCGTCTG 59.558 55.0 0.00 0.0 0.0 3.51 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
171 172 0.881118 TTTTGAGCGAACAGGGATGC 59.119 50.000 0.00 0.00 0.00 3.91
174 175 1.817099 GAGCGAACAGGGATGCTGG 60.817 63.158 0.00 0.00 37.91 4.85
175 176 3.512516 GCGAACAGGGATGCTGGC 61.513 66.667 0.00 0.00 0.00 4.85
176 177 2.825836 CGAACAGGGATGCTGGCC 60.826 66.667 0.00 0.00 0.00 5.36
177 178 2.440980 GAACAGGGATGCTGGCCC 60.441 66.667 0.00 0.00 46.40 5.80
191 195 1.152546 GGCCCAGTCAAACTTGGGT 60.153 57.895 10.95 0.00 38.21 4.51
220 224 1.009335 GAACAAAACGGGCCGTCAC 60.009 57.895 34.23 15.54 39.99 3.67
221 225 2.704973 GAACAAAACGGGCCGTCACG 62.705 60.000 34.23 24.10 39.99 4.35
308 340 0.673985 GGCCAACCTTTTTCTTCGCT 59.326 50.000 0.00 0.00 0.00 4.93
309 341 1.602920 GGCCAACCTTTTTCTTCGCTG 60.603 52.381 0.00 0.00 0.00 5.18
310 342 1.770957 CCAACCTTTTTCTTCGCTGC 58.229 50.000 0.00 0.00 0.00 5.25
311 343 1.398595 CAACCTTTTTCTTCGCTGCG 58.601 50.000 17.25 17.25 0.00 5.18
312 344 1.002900 CAACCTTTTTCTTCGCTGCGA 60.003 47.619 22.24 22.24 0.00 5.10
313 345 0.586802 ACCTTTTTCTTCGCTGCGAC 59.413 50.000 25.94 0.00 34.89 5.19
314 346 0.868406 CCTTTTTCTTCGCTGCGACT 59.132 50.000 25.94 0.00 34.89 4.18
315 347 1.136224 CCTTTTTCTTCGCTGCGACTC 60.136 52.381 25.94 0.00 34.89 3.36
359 391 3.567797 GATCGCCAAGGACGCAGC 61.568 66.667 0.00 0.00 0.00 5.25
396 432 1.394618 AGAGCTCTCCGTACCATCAC 58.605 55.000 11.45 0.00 0.00 3.06
423 459 3.399330 TCGTTGTCCACTCCATCTTTTC 58.601 45.455 0.00 0.00 0.00 2.29
452 488 3.652000 GACGCCCGTTTTTCGCCA 61.652 61.111 0.00 0.00 38.35 5.69
502 540 3.618774 GTACCGTACGGCAGAAGAG 57.381 57.895 33.62 8.30 39.32 2.85
503 541 1.089920 GTACCGTACGGCAGAAGAGA 58.910 55.000 33.62 6.45 39.32 3.10
504 542 1.674962 GTACCGTACGGCAGAAGAGAT 59.325 52.381 33.62 13.62 39.32 2.75
572 633 0.328258 TTCTCCCTAAGCAACTGCCC 59.672 55.000 0.00 0.00 43.38 5.36
573 634 1.450312 CTCCCTAAGCAACTGCCCG 60.450 63.158 0.00 0.00 43.38 6.13
574 635 3.134127 CCCTAAGCAACTGCCCGC 61.134 66.667 0.00 0.00 43.38 6.13
575 636 3.134127 CCTAAGCAACTGCCCGCC 61.134 66.667 0.00 0.00 43.38 6.13
576 637 2.045926 CTAAGCAACTGCCCGCCT 60.046 61.111 0.00 0.00 43.38 5.52
598 659 3.952628 CTTGCCCTCCCGTTCCGTC 62.953 68.421 0.00 0.00 0.00 4.79
636 697 1.654954 CTGGGTAGACTCGTCCCACG 61.655 65.000 9.33 0.00 45.19 4.94
821 1182 0.109412 GGCGTTACGTAGCACTCTGT 60.109 55.000 10.16 0.00 34.54 3.41
822 1183 1.257539 GCGTTACGTAGCACTCTGTC 58.742 55.000 10.16 0.00 0.00 3.51
823 1184 1.135746 GCGTTACGTAGCACTCTGTCT 60.136 52.381 10.16 0.00 0.00 3.41
824 1185 2.506865 CGTTACGTAGCACTCTGTCTG 58.493 52.381 10.16 0.00 0.00 3.51
835 1196 3.774066 CACTCTGTCTGACGCATCAATA 58.226 45.455 2.98 0.00 33.30 1.90
836 1197 3.795639 CACTCTGTCTGACGCATCAATAG 59.204 47.826 2.98 0.00 33.30 1.73
884 1249 0.252742 TCTCCCTCCACTTCCTTCCC 60.253 60.000 0.00 0.00 0.00 3.97
885 1250 0.252927 CTCCCTCCACTTCCTTCCCT 60.253 60.000 0.00 0.00 0.00 4.20
886 1251 0.252742 TCCCTCCACTTCCTTCCCTC 60.253 60.000 0.00 0.00 0.00 4.30
889 1254 0.252927 CTCCACTTCCTTCCCTCCCT 60.253 60.000 0.00 0.00 0.00 4.20
890 1255 1.008449 CTCCACTTCCTTCCCTCCCTA 59.992 57.143 0.00 0.00 0.00 3.53
891 1256 1.008449 TCCACTTCCTTCCCTCCCTAG 59.992 57.143 0.00 0.00 0.00 3.02
892 1257 1.273896 CCACTTCCTTCCCTCCCTAGT 60.274 57.143 0.00 0.00 0.00 2.57
893 1258 2.112190 CACTTCCTTCCCTCCCTAGTC 58.888 57.143 0.00 0.00 0.00 2.59
894 1259 2.012236 ACTTCCTTCCCTCCCTAGTCT 58.988 52.381 0.00 0.00 0.00 3.24
895 1260 2.292587 ACTTCCTTCCCTCCCTAGTCTG 60.293 54.545 0.00 0.00 0.00 3.51
896 1261 1.695065 TCCTTCCCTCCCTAGTCTGA 58.305 55.000 0.00 0.00 0.00 3.27
897 1262 1.571457 TCCTTCCCTCCCTAGTCTGAG 59.429 57.143 0.00 0.00 0.00 3.35
924 1289 2.202544 GAGACCAGAGCTCGCACG 60.203 66.667 8.37 0.00 0.00 5.34
1383 1773 4.681978 AACGTGTGCCCGCTCCTC 62.682 66.667 0.00 0.00 0.00 3.71
1937 2347 6.751157 TGTCTGCAATGTTTCTTGATTGATT 58.249 32.000 0.00 0.00 32.24 2.57
2130 2540 2.217038 GCCCCAGGTCAGTCACTCA 61.217 63.158 0.00 0.00 0.00 3.41
2131 2541 1.674057 CCCCAGGTCAGTCACTCAC 59.326 63.158 0.00 0.00 0.00 3.51
2132 2542 1.121407 CCCCAGGTCAGTCACTCACA 61.121 60.000 0.00 0.00 0.00 3.58
2133 2543 0.034059 CCCAGGTCAGTCACTCACAC 59.966 60.000 0.00 0.00 0.00 3.82
2134 2544 1.043816 CCAGGTCAGTCACTCACACT 58.956 55.000 0.00 0.00 0.00 3.55
2135 2545 1.000283 CCAGGTCAGTCACTCACACTC 60.000 57.143 0.00 0.00 0.00 3.51
2136 2546 1.683385 CAGGTCAGTCACTCACACTCA 59.317 52.381 0.00 0.00 0.00 3.41
2137 2547 1.683917 AGGTCAGTCACTCACACTCAC 59.316 52.381 0.00 0.00 0.00 3.51
2138 2548 1.683917 GGTCAGTCACTCACACTCACT 59.316 52.381 0.00 0.00 0.00 3.41
2139 2549 2.287909 GGTCAGTCACTCACACTCACTC 60.288 54.545 0.00 0.00 0.00 3.51
2146 2556 2.740055 CACACTCACTCAGCCGCC 60.740 66.667 0.00 0.00 0.00 6.13
2195 2618 3.503363 GCCCTGACGCATGCAGAC 61.503 66.667 19.57 11.25 35.39 3.51
2508 2936 3.122255 GCAGCGCGCGTTAATTAATTAAC 60.122 43.478 32.35 29.36 45.27 2.01
2710 3145 4.777896 TCCATGACAGAGGTAAGCTTACTT 59.222 41.667 30.36 25.66 40.07 2.24
2715 3150 4.714632 ACAGAGGTAAGCTTACTTGCAAA 58.285 39.130 30.36 0.00 40.01 3.68
2717 3152 6.472887 ACAGAGGTAAGCTTACTTGCAAATA 58.527 36.000 30.36 0.00 40.01 1.40
2719 3154 8.265055 ACAGAGGTAAGCTTACTTGCAAATATA 58.735 33.333 30.36 0.00 40.01 0.86
2720 3155 9.277783 CAGAGGTAAGCTTACTTGCAAATATAT 57.722 33.333 30.36 7.36 40.01 0.86
2749 3184 5.970317 ATATATGCACACATCACAATGGG 57.030 39.130 0.00 0.00 42.39 4.00
2757 3192 3.206150 CACATCACAATGGGTAGTAGGC 58.794 50.000 0.00 0.00 37.19 3.93
2758 3193 3.115390 ACATCACAATGGGTAGTAGGCT 58.885 45.455 0.00 0.00 37.19 4.58
2759 3194 3.523564 ACATCACAATGGGTAGTAGGCTT 59.476 43.478 0.00 0.00 37.19 4.35
2760 3195 3.627395 TCACAATGGGTAGTAGGCTTG 57.373 47.619 0.00 0.00 0.00 4.01
2761 3196 2.238646 TCACAATGGGTAGTAGGCTTGG 59.761 50.000 0.00 0.00 0.00 3.61
2762 3197 1.064685 ACAATGGGTAGTAGGCTTGGC 60.065 52.381 0.00 0.00 0.00 4.52
2763 3198 0.180406 AATGGGTAGTAGGCTTGGCG 59.820 55.000 0.00 0.00 0.00 5.69
2764 3199 2.203029 GGGTAGTAGGCTTGGCGC 60.203 66.667 0.00 0.00 38.13 6.53
2765 3200 2.585247 GGTAGTAGGCTTGGCGCG 60.585 66.667 0.00 0.00 40.44 6.86
2766 3201 2.493030 GTAGTAGGCTTGGCGCGA 59.507 61.111 12.10 0.00 40.44 5.87
2767 3202 1.589196 GTAGTAGGCTTGGCGCGAG 60.589 63.158 12.10 0.00 40.44 5.03
2768 3203 2.050350 TAGTAGGCTTGGCGCGAGT 61.050 57.895 12.10 0.00 40.44 4.18
2769 3204 0.749091 TAGTAGGCTTGGCGCGAGTA 60.749 55.000 12.10 0.00 40.44 2.59
2787 3222 2.356382 AGTAGCTAGCACATGTCTCGAC 59.644 50.000 18.83 0.00 0.00 4.20
2848 3291 1.202320 GCGGGTAACAACGTTGACG 59.798 57.895 33.66 25.49 42.26 4.35
2850 3293 0.503961 CGGGTAACAACGTTGACGAC 59.496 55.000 33.66 24.22 40.27 4.34
2872 3325 2.051423 TGCGTCGAATAATCTGATCGC 58.949 47.619 9.75 9.75 42.17 4.58
2873 3326 2.051423 GCGTCGAATAATCTGATCGCA 58.949 47.619 11.26 0.00 41.59 5.10
2876 3329 4.464112 CGTCGAATAATCTGATCGCAGTA 58.536 43.478 0.00 0.00 42.84 2.74
3052 3508 1.527380 GCCGTCCCCTTTGTCAACA 60.527 57.895 0.00 0.00 0.00 3.33
3063 3519 2.957402 TTGTCAACATCCTCAGCCTT 57.043 45.000 0.00 0.00 0.00 4.35
3092 3553 2.006772 CACGGGCTAAGATTGCGTC 58.993 57.895 0.00 0.00 0.00 5.19
3099 3560 1.849219 GCTAAGATTGCGTCAGACGAG 59.151 52.381 27.29 13.54 46.05 4.18
3100 3561 2.732597 GCTAAGATTGCGTCAGACGAGT 60.733 50.000 27.29 10.83 46.05 4.18
3117 3578 2.161012 CGAGTGTGATGCTTGCTGAAAT 59.839 45.455 0.00 0.00 0.00 2.17
3225 3712 2.376181 AGTAAAAACCACCCCCGTATGT 59.624 45.455 0.00 0.00 0.00 2.29
3290 3815 1.830587 AATGCAGGCAGAGACCGACA 61.831 55.000 0.00 0.00 33.69 4.35
3394 3960 1.519408 ACGTGCCGCTTTCATTACTT 58.481 45.000 0.00 0.00 0.00 2.24
3395 3961 2.690786 ACGTGCCGCTTTCATTACTTA 58.309 42.857 0.00 0.00 0.00 2.24
3469 4046 2.731691 TTCGGGACAGGTTGAGCTGC 62.732 60.000 9.91 0.00 0.00 5.25
3490 4067 1.616628 CCCTACCCTGGCTCCTTGT 60.617 63.158 0.00 0.00 0.00 3.16
3542 4119 1.737838 CATGCTCCTCGTAAAAGGCA 58.262 50.000 0.00 0.00 36.29 4.75
3550 4127 2.510613 CTCGTAAAAGGCAAGGGGAAA 58.489 47.619 0.00 0.00 0.00 3.13
3551 4128 2.228103 CTCGTAAAAGGCAAGGGGAAAC 59.772 50.000 0.00 0.00 0.00 2.78
3552 4129 1.957877 CGTAAAAGGCAAGGGGAAACA 59.042 47.619 0.00 0.00 0.00 2.83
3555 4132 0.471780 AAAGGCAAGGGGAAACAGGG 60.472 55.000 0.00 0.00 0.00 4.45
3556 4133 2.283894 GGCAAGGGGAAACAGGGG 60.284 66.667 0.00 0.00 0.00 4.79
3557 4134 2.526110 GCAAGGGGAAACAGGGGT 59.474 61.111 0.00 0.00 0.00 4.95
3641 4223 3.010027 TCCCATGCAAGGTGTTCATCTTA 59.990 43.478 7.29 0.00 0.00 2.10
3645 4227 5.589855 CCATGCAAGGTGTTCATCTTATACA 59.410 40.000 0.00 0.00 0.00 2.29
3646 4228 6.095300 CCATGCAAGGTGTTCATCTTATACAA 59.905 38.462 0.00 0.00 0.00 2.41
3647 4229 6.494893 TGCAAGGTGTTCATCTTATACAAC 57.505 37.500 0.00 0.00 0.00 3.32
3648 4230 6.000840 TGCAAGGTGTTCATCTTATACAACA 58.999 36.000 0.00 0.00 31.97 3.33
3673 4255 7.133891 ACAACTTGCTTATCAGTAACATGTC 57.866 36.000 0.00 0.00 0.00 3.06
3717 4299 7.652727 ACAAGCAACCTCTTCTTTCTTTAATC 58.347 34.615 0.00 0.00 0.00 1.75
3773 4355 2.040412 AGGGAGATTTTGCTCGGAAAGT 59.960 45.455 0.00 0.00 35.74 2.66
3878 4464 3.709653 CACTCCTAAATACTGGCCAGGTA 59.290 47.826 35.42 24.00 0.00 3.08
3883 4501 5.542635 TCCTAAATACTGGCCAGGTAGTATG 59.457 44.000 35.42 18.70 39.40 2.39
3891 4509 5.074652 ACTGGCCAGGTAGTATGATAGTAGA 59.925 44.000 35.42 0.00 0.00 2.59
3957 4576 3.562779 TTCGGTCGGTCGGTGCTTC 62.563 63.158 0.00 0.00 0.00 3.86
3987 4606 2.342650 CCGCCAACACCATTCTGGG 61.343 63.158 0.00 0.00 43.37 4.45
3988 4621 1.603455 CGCCAACACCATTCTGGGT 60.603 57.895 0.00 0.00 43.37 4.51
4031 4664 5.042593 CACTCTCATCTGACAGAATACTGC 58.957 45.833 9.70 0.00 46.95 4.40
4038 4673 3.258372 TCTGACAGAATACTGCGGTTTCT 59.742 43.478 1.99 10.14 46.95 2.52
4039 4674 3.997021 CTGACAGAATACTGCGGTTTCTT 59.003 43.478 1.99 4.69 46.95 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 3.895704 AAGGAGCTTACCCCTCAAAAA 57.104 42.857 0.00 0.00 31.17 1.94
132 133 3.895704 AAAGGAGCTTACCCCTCAAAA 57.104 42.857 0.00 0.00 31.17 2.44
159 160 2.825836 GGCCAGCATCCCTGTTCG 60.826 66.667 0.00 0.00 40.06 3.95
166 167 1.304381 TTTGACTGGGCCAGCATCC 60.304 57.895 33.04 19.16 34.37 3.51
167 168 0.610232 AGTTTGACTGGGCCAGCATC 60.610 55.000 33.04 23.45 34.37 3.91
168 169 0.178953 AAGTTTGACTGGGCCAGCAT 60.179 50.000 33.04 15.50 34.37 3.79
169 170 1.108727 CAAGTTTGACTGGGCCAGCA 61.109 55.000 33.04 26.55 34.37 4.41
171 172 1.181098 CCCAAGTTTGACTGGGCCAG 61.181 60.000 31.62 31.62 38.02 4.85
174 175 1.179174 GGACCCAAGTTTGACTGGGC 61.179 60.000 7.06 0.72 38.02 5.36
175 176 0.889186 CGGACCCAAGTTTGACTGGG 60.889 60.000 5.57 5.57 39.12 4.45
176 177 0.107831 TCGGACCCAAGTTTGACTGG 59.892 55.000 0.00 0.00 0.00 4.00
177 178 1.873591 CTTCGGACCCAAGTTTGACTG 59.126 52.381 0.00 0.00 0.00 3.51
191 195 0.578211 GTTTTGTTCGACGCTTCGGA 59.422 50.000 13.04 0.00 45.90 4.55
282 286 1.341209 GAAAAAGGTTGGCCTGTCAGG 59.659 52.381 15.15 15.15 46.33 3.86
285 289 2.287608 CGAAGAAAAAGGTTGGCCTGTC 60.288 50.000 3.32 0.00 46.33 3.51
286 290 1.681264 CGAAGAAAAAGGTTGGCCTGT 59.319 47.619 3.32 0.00 46.33 4.00
287 291 1.602920 GCGAAGAAAAAGGTTGGCCTG 60.603 52.381 3.32 0.00 46.33 4.85
359 391 1.536766 TCTTCCGCTGCATTTGTCAAG 59.463 47.619 0.00 0.00 0.00 3.02
387 423 0.461339 AACGATGCGGGTGATGGTAC 60.461 55.000 0.00 0.00 0.00 3.34
396 432 2.047274 AGTGGACAACGATGCGGG 60.047 61.111 0.00 0.00 0.00 6.13
466 502 2.772691 CGTACCCCTGGCTCGTCTC 61.773 68.421 0.00 0.00 0.00 3.36
498 536 3.304829 GGAAGGGACTCTGCTATCTCTT 58.695 50.000 0.00 0.00 38.49 2.85
499 537 2.425683 GGGAAGGGACTCTGCTATCTCT 60.426 54.545 0.00 0.00 38.49 3.10
500 538 1.967779 GGGAAGGGACTCTGCTATCTC 59.032 57.143 0.00 0.00 38.49 2.75
502 540 2.095604 AGGGAAGGGACTCTGCTATC 57.904 55.000 0.00 0.00 38.49 2.08
503 541 2.403561 GAAGGGAAGGGACTCTGCTAT 58.596 52.381 0.00 0.00 38.49 2.97
504 542 1.622725 GGAAGGGAAGGGACTCTGCTA 60.623 57.143 0.00 0.00 38.49 3.49
534 593 2.258726 GGGAAGGAAGCGTTGCGTT 61.259 57.895 0.00 0.00 0.00 4.84
575 636 3.868200 AACGGGAGGGCAAGGCAAG 62.868 63.158 0.00 0.00 0.00 4.01
576 637 3.860930 GAACGGGAGGGCAAGGCAA 62.861 63.158 0.00 0.00 0.00 4.52
615 676 3.516911 GGGACGAGTCTACCCAGAT 57.483 57.895 14.16 0.00 42.81 2.90
636 697 4.314440 TGACACCTGAGCGTGGCC 62.314 66.667 0.00 0.00 41.44 5.36
821 1182 0.106708 GGGGCTATTGATGCGTCAGA 59.893 55.000 8.93 0.65 35.39 3.27
822 1183 0.886490 GGGGGCTATTGATGCGTCAG 60.886 60.000 8.93 0.00 35.39 3.51
823 1184 1.148273 GGGGGCTATTGATGCGTCA 59.852 57.895 3.97 3.97 0.00 4.35
824 1185 4.065110 GGGGGCTATTGATGCGTC 57.935 61.111 0.00 0.00 0.00 5.19
842 1207 0.687354 AGTGGTGTAGGAAGTGGCTG 59.313 55.000 0.00 0.00 0.00 4.85
884 1249 3.181448 GGGTAGAGACTCAGACTAGGGAG 60.181 56.522 5.02 0.64 37.18 4.30
885 1250 2.778850 GGGTAGAGACTCAGACTAGGGA 59.221 54.545 5.02 0.00 0.00 4.20
886 1251 2.485835 CGGGTAGAGACTCAGACTAGGG 60.486 59.091 5.02 0.00 0.00 3.53
941 1322 2.103042 GCGCGGCTTCTTGACTGAT 61.103 57.895 8.83 0.00 0.00 2.90
946 1327 3.711842 CGTTGCGCGGCTTCTTGA 61.712 61.111 8.83 0.00 36.85 3.02
996 1377 2.202878 TACAGCGGCTTCATCGGC 60.203 61.111 0.00 0.00 0.00 5.54
1917 2307 9.708092 TTCATTAATCAATCAAGAAACATTGCA 57.292 25.926 0.00 0.00 31.15 4.08
1937 2347 2.874086 CCGTCTGAGCATGCATTCATTA 59.126 45.455 21.98 4.41 0.00 1.90
2130 2540 4.363990 CGGCGGCTGAGTGAGTGT 62.364 66.667 7.61 0.00 0.00 3.55
2133 2543 4.827087 ATGCGGCGGCTGAGTGAG 62.827 66.667 17.76 0.00 40.82 3.51
2134 2544 4.819761 GATGCGGCGGCTGAGTGA 62.820 66.667 17.76 0.00 40.82 3.41
2135 2545 4.827087 AGATGCGGCGGCTGAGTG 62.827 66.667 17.76 0.00 40.82 3.51
2136 2546 4.521062 GAGATGCGGCGGCTGAGT 62.521 66.667 17.76 0.00 40.82 3.41
2139 2549 4.923942 ATGGAGATGCGGCGGCTG 62.924 66.667 17.76 3.95 40.82 4.85
2146 2556 0.730834 GGATCGACGATGGAGATGCG 60.731 60.000 16.49 0.00 0.00 4.73
2195 2618 4.313522 CGAAGTCGGAGATCTGTTTTTG 57.686 45.455 0.00 0.00 40.67 2.44
2296 2724 2.277756 CCGCGCGTGTAGTACTCC 60.278 66.667 29.95 0.00 0.00 3.85
2429 2857 3.897141 AAATGTTTGGTTGGTCGGTTT 57.103 38.095 0.00 0.00 0.00 3.27
2508 2936 5.756950 TCGCGTTGTTTAGACAAGATTAG 57.243 39.130 5.77 0.00 45.86 1.73
2519 2951 0.109964 GCCTGCATTCGCGTTGTTTA 60.110 50.000 5.77 0.00 42.97 2.01
2723 3158 9.346005 CCCATTGTGATGTGTGCATATATATAT 57.654 33.333 0.00 0.00 35.07 0.86
2724 3159 8.328014 ACCCATTGTGATGTGTGCATATATATA 58.672 33.333 0.00 0.00 35.07 0.86
2725 3160 7.177184 ACCCATTGTGATGTGTGCATATATAT 58.823 34.615 0.00 0.00 35.07 0.86
2726 3161 6.541907 ACCCATTGTGATGTGTGCATATATA 58.458 36.000 0.00 0.00 35.07 0.86
2727 3162 5.387788 ACCCATTGTGATGTGTGCATATAT 58.612 37.500 0.00 0.00 35.07 0.86
2728 3163 4.790937 ACCCATTGTGATGTGTGCATATA 58.209 39.130 0.00 0.00 35.07 0.86
2729 3164 3.634504 ACCCATTGTGATGTGTGCATAT 58.365 40.909 0.00 0.00 35.07 1.78
2730 3165 3.084536 ACCCATTGTGATGTGTGCATA 57.915 42.857 0.00 0.00 35.07 3.14
2731 3166 1.927487 ACCCATTGTGATGTGTGCAT 58.073 45.000 0.00 0.00 38.18 3.96
2737 3172 3.115390 AGCCTACTACCCATTGTGATGT 58.885 45.455 0.00 0.00 0.00 3.06
2738 3173 3.845781 AGCCTACTACCCATTGTGATG 57.154 47.619 0.00 0.00 0.00 3.07
2748 3183 2.585247 CGCGCCAAGCCTACTACC 60.585 66.667 0.00 0.00 44.76 3.18
2749 3184 1.589196 CTCGCGCCAAGCCTACTAC 60.589 63.158 0.00 0.00 44.76 2.73
2750 3185 0.749091 TACTCGCGCCAAGCCTACTA 60.749 55.000 0.00 0.00 44.76 1.82
2751 3186 2.005960 CTACTCGCGCCAAGCCTACT 62.006 60.000 0.00 0.00 44.76 2.57
2752 3187 1.589196 CTACTCGCGCCAAGCCTAC 60.589 63.158 0.00 0.00 44.76 3.18
2753 3188 2.805546 CTACTCGCGCCAAGCCTA 59.194 61.111 0.00 0.00 44.76 3.93
2754 3189 4.821589 GCTACTCGCGCCAAGCCT 62.822 66.667 0.00 0.00 44.76 4.58
2755 3190 3.426117 TAGCTACTCGCGCCAAGCC 62.426 63.158 18.53 5.63 45.59 4.35
2756 3191 1.946650 CTAGCTACTCGCGCCAAGC 60.947 63.158 15.64 15.64 45.59 4.01
2757 3192 1.946650 GCTAGCTACTCGCGCCAAG 60.947 63.158 7.70 1.65 45.59 3.61
2758 3193 2.104331 GCTAGCTACTCGCGCCAA 59.896 61.111 7.70 0.00 45.59 4.52
2759 3194 3.138128 TGCTAGCTACTCGCGCCA 61.138 61.111 17.23 0.00 45.59 5.69
2760 3195 2.655685 GTGCTAGCTACTCGCGCC 60.656 66.667 17.23 0.00 45.59 6.53
2761 3196 1.299468 ATGTGCTAGCTACTCGCGC 60.299 57.895 17.23 9.43 45.59 6.86
2762 3197 0.248661 ACATGTGCTAGCTACTCGCG 60.249 55.000 17.23 0.00 45.59 5.87
2763 3198 1.066303 AGACATGTGCTAGCTACTCGC 59.934 52.381 17.23 1.78 39.57 5.03
2764 3199 2.601029 CGAGACATGTGCTAGCTACTCG 60.601 54.545 17.23 19.40 39.49 4.18
2765 3200 2.614520 TCGAGACATGTGCTAGCTACTC 59.385 50.000 17.23 13.01 0.00 2.59
2766 3201 2.356382 GTCGAGACATGTGCTAGCTACT 59.644 50.000 17.23 6.01 0.00 2.57
2767 3202 2.722071 GTCGAGACATGTGCTAGCTAC 58.278 52.381 17.23 12.72 0.00 3.58
2768 3203 1.330829 CGTCGAGACATGTGCTAGCTA 59.669 52.381 17.23 5.45 0.00 3.32
2769 3204 0.099613 CGTCGAGACATGTGCTAGCT 59.900 55.000 17.23 0.00 0.00 3.32
2848 3291 4.201438 CGATCAGATTATTCGACGCATGTC 60.201 45.833 0.00 0.00 41.91 3.06
2850 3293 3.480985 GCGATCAGATTATTCGACGCATG 60.481 47.826 0.00 0.00 43.35 4.06
2856 3309 4.023193 TGCTACTGCGATCAGATTATTCGA 60.023 41.667 0.00 0.00 42.95 3.71
2965 3418 4.790962 TCCTCCCCCTCGTCGTCG 62.791 72.222 0.00 0.00 38.55 5.12
3019 3472 4.467084 GGCGTGCCGGATTCCTCA 62.467 66.667 5.05 0.00 0.00 3.86
3063 3519 2.047274 GCCCGTGCTAAGTGCTCA 60.047 61.111 0.00 0.00 43.37 4.26
3092 3553 0.441533 GCAAGCATCACACTCGTCTG 59.558 55.000 0.00 0.00 0.00 3.51
3099 3560 5.437263 CAAAAATTTCAGCAAGCATCACAC 58.563 37.500 0.00 0.00 0.00 3.82
3100 3561 4.024725 GCAAAAATTTCAGCAAGCATCACA 60.025 37.500 9.25 0.00 0.00 3.58
3117 3578 1.703411 CAGGTGGGAAGGAGCAAAAA 58.297 50.000 0.00 0.00 0.00 1.94
3144 3605 3.915437 ACGAAAAGCCTTTACATGTGG 57.085 42.857 9.11 1.98 0.00 4.17
3145 3606 4.606961 ACAACGAAAAGCCTTTACATGTG 58.393 39.130 9.11 0.00 0.00 3.21
3146 3607 4.553938 CGACAACGAAAAGCCTTTACATGT 60.554 41.667 2.69 2.69 42.66 3.21
3148 3609 3.810941 TCGACAACGAAAAGCCTTTACAT 59.189 39.130 0.00 0.00 45.74 2.29
3149 3610 3.196463 TCGACAACGAAAAGCCTTTACA 58.804 40.909 0.00 0.00 45.74 2.41
3225 3712 1.589461 CCGTTCGTGTCGTGGTCAA 60.589 57.895 0.00 0.00 0.00 3.18
3270 3760 0.674895 GTCGGTCTCTGCCTGCATTT 60.675 55.000 0.00 0.00 0.00 2.32
3277 3767 2.574399 GGTCTGTCGGTCTCTGCC 59.426 66.667 0.00 0.00 0.00 4.85
3278 3768 2.179517 CGGTCTGTCGGTCTCTGC 59.820 66.667 0.00 0.00 0.00 4.26
3279 3769 1.502640 GTCGGTCTGTCGGTCTCTG 59.497 63.158 0.00 0.00 0.00 3.35
3290 3815 3.386237 GAGCAGGCAGGTCGGTCT 61.386 66.667 0.00 0.00 34.67 3.85
3490 4067 0.901580 GGGTCCGTCCAAGAGGTGTA 60.902 60.000 0.00 0.00 38.11 2.90
3533 4110 2.299013 CCTGTTTCCCCTTGCCTTTTAC 59.701 50.000 0.00 0.00 0.00 2.01
3542 4119 0.845102 ATCGACCCCTGTTTCCCCTT 60.845 55.000 0.00 0.00 0.00 3.95
3550 4127 0.676184 CATGATCGATCGACCCCTGT 59.324 55.000 22.06 2.53 0.00 4.00
3551 4128 0.676184 ACATGATCGATCGACCCCTG 59.324 55.000 22.06 18.81 0.00 4.45
3552 4129 0.676184 CACATGATCGATCGACCCCT 59.324 55.000 22.06 3.88 0.00 4.79
3555 4132 0.946221 GGCCACATGATCGATCGACC 60.946 60.000 22.06 12.29 0.00 4.79
3556 4133 1.278172 CGGCCACATGATCGATCGAC 61.278 60.000 22.06 14.65 0.00 4.20
3557 4134 1.007387 CGGCCACATGATCGATCGA 60.007 57.895 21.86 21.86 0.00 3.59
3641 4223 7.510549 ACTGATAAGCAAGTTGTTGTTGTAT 57.489 32.000 4.48 0.00 35.92 2.29
3645 4227 7.328277 TGTTACTGATAAGCAAGTTGTTGTT 57.672 32.000 4.48 0.00 35.92 2.83
3646 4228 6.935741 TGTTACTGATAAGCAAGTTGTTGT 57.064 33.333 4.48 0.00 35.92 3.32
3647 4229 7.362662 ACATGTTACTGATAAGCAAGTTGTTG 58.637 34.615 4.48 0.00 36.67 3.33
3648 4230 7.445402 AGACATGTTACTGATAAGCAAGTTGTT 59.555 33.333 0.00 0.00 0.00 2.83
3773 4355 8.426569 ACTGTATCCCACTTTAGTACTTTACA 57.573 34.615 0.00 0.00 0.00 2.41
3891 4509 6.127140 ACGCCACTACTATTCCTGAATAAACT 60.127 38.462 1.60 0.00 33.34 2.66
3987 4606 2.736192 GCTTCAGAGTTCAGAGCTCAAC 59.264 50.000 17.77 12.52 35.55 3.18
3988 4621 2.366590 TGCTTCAGAGTTCAGAGCTCAA 59.633 45.455 17.77 0.00 35.55 3.02
4031 4664 5.270853 CAACAGGTGTAGAAAAAGAAACCG 58.729 41.667 0.00 0.00 32.83 4.44
4038 4673 3.311322 CAGTCGCAACAGGTGTAGAAAAA 59.689 43.478 0.00 0.00 0.00 1.94
4039 4674 2.869801 CAGTCGCAACAGGTGTAGAAAA 59.130 45.455 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.