Multiple sequence alignment - TraesCS6A01G417700

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 TraesCS6A01G417700 chr6A 100.000 3197 0 0 1 3197 615891389 615888193 0.000000e+00 5904.0
1 TraesCS6A01G417700 chr6A 83.019 106 6 10 2752 2851 615888539 615888638 5.680000e-13 86.1
2 TraesCS6A01G417700 chr6D 90.918 2984 197 25 1 2965 471072670 471069742 0.000000e+00 3941.0
3 TraesCS6A01G417700 chr6D 76.770 452 84 14 1 437 315365831 315366276 1.920000e-57 233.0
4 TraesCS6A01G417700 chr6B 91.475 2604 161 27 4 2581 719507583 719510151 0.000000e+00 3522.0
5 TraesCS6A01G417700 chr6B 87.352 506 45 9 2689 3194 719515607 719516093 2.150000e-156 562.0
6 TraesCS6A01G417700 chr6B 89.474 342 24 7 2850 3191 719510467 719510796 3.810000e-114 422.0
7 TraesCS6A01G417700 chr6B 85.065 154 14 5 2527 2680 719515373 719515517 7.150000e-32 148.0
8 TraesCS6A01G417700 chr5D 82.463 268 43 4 126 391 441401650 441401915 6.900000e-57 231.0
9 TraesCS6A01G417700 chr5D 76.063 447 84 16 15 450 512448169 512447735 8.990000e-51 211.0
10 TraesCS6A01G417700 chr4A 76.282 468 86 13 15 466 575005514 575005056 3.210000e-55 226.0
11 TraesCS6A01G417700 chr4D 75.658 456 94 12 1 444 354115338 354114888 8.990000e-51 211.0
12 TraesCS6A01G417700 chr4D 100.000 33 0 0 2752 2784 58640761 58640729 9.580000e-06 62.1
13 TraesCS6A01G417700 chr7B 78.593 327 62 5 120 446 34069388 34069706 3.230000e-50 209.0
14 TraesCS6A01G417700 chr7B 97.143 35 1 0 2750 2784 537577277 537577311 3.440000e-05 60.2
15 TraesCS6A01G417700 chr3A 78.419 329 64 6 115 441 486930416 486930739 1.160000e-49 207.0
16 TraesCS6A01G417700 chr1B 96.000 75 2 1 2784 2858 554241265 554241192 1.560000e-23 121.0
17 TraesCS6A01G417700 chr3D 95.946 74 2 1 2786 2859 508471364 508471292 5.600000e-23 119.0
18 TraesCS6A01G417700 chr2A 95.652 69 3 0 2784 2852 632931712 632931780 9.370000e-21 111.0
19 TraesCS6A01G417700 chr1A 95.652 69 3 0 2784 2852 42512565 42512633 9.370000e-21 111.0
20 TraesCS6A01G417700 chr2B 94.286 70 4 0 2784 2853 724550991 724550922 1.210000e-19 108.0
21 TraesCS6A01G417700 chr5B 94.203 69 4 0 2783 2851 216845527 216845459 4.360000e-19 106.0
22 TraesCS6A01G417700 chr5A 91.549 71 6 0 2784 2854 333742932 333742862 7.300000e-17 99.0
23 TraesCS6A01G417700 chr5A 97.222 36 1 0 2753 2788 627516484 627516519 9.580000e-06 62.1
24 TraesCS6A01G417700 chr4B 100.000 33 0 0 2752 2784 37385498 37385466 9.580000e-06 62.1
25 TraesCS6A01G417700 chr3B 100.000 33 0 0 2752 2784 26780031 26779999 9.580000e-06 62.1
26 TraesCS6A01G417700 chr3B 97.222 36 1 0 2753 2788 583354064 583354099 9.580000e-06 62.1
27 TraesCS6A01G417700 chr7D 94.872 39 1 1 2750 2788 8008338 8008375 3.440000e-05 60.2


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 TraesCS6A01G417700 chr6A 615888193 615891389 3196 True 5904 5904 100.0000 1 3197 1 chr6A.!!$R1 3196
1 TraesCS6A01G417700 chr6D 471069742 471072670 2928 True 3941 3941 90.9180 1 2965 1 chr6D.!!$R1 2964
2 TraesCS6A01G417700 chr6B 719507583 719510796 3213 False 1972 3522 90.4745 4 3191 2 chr6B.!!$F1 3187
3 TraesCS6A01G417700 chr6B 719515373 719516093 720 False 355 562 86.2085 2527 3194 2 chr6B.!!$F2 667

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
607 621 0.033208 ACTGGAGAGAGGCAGAGAGG 60.033 60.0 0.0 0.0 0.00 3.69 F
1613 1634 0.250467 ATCGCCGATGGGAAAGATGG 60.250 55.0 0.0 0.0 36.96 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1819 0.602562 TTAACAATGTGCCTGCTGCC 59.397 50.0 0.0 0.0 40.16 4.85 R
3016 3187 0.179000 ATAGCCTTCAACCGCCTGAG 59.821 55.0 0.0 0.0 0.00 3.35 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
29 30 6.232581 ACTCTCTAAAGATGGAATGAGGTG 57.767 41.667 0.00 0.00 0.00 4.00
32 33 5.190528 TCTCTAAAGATGGAATGAGGTGCTT 59.809 40.000 0.00 0.00 0.00 3.91
36 37 1.002069 ATGGAATGAGGTGCTTCCCA 58.998 50.000 0.00 0.00 40.22 4.37
37 38 1.002069 TGGAATGAGGTGCTTCCCAT 58.998 50.000 0.00 0.00 40.22 4.00
41 42 3.117888 GGAATGAGGTGCTTCCCATCTAA 60.118 47.826 0.00 0.00 34.22 2.10
46 47 0.106669 GTGCTTCCCATCTAACCCCC 60.107 60.000 0.00 0.00 0.00 5.40
51 52 1.691337 CCCATCTAACCCCCGTCCA 60.691 63.158 0.00 0.00 0.00 4.02
84 85 0.109551 ATGTCGTCAGAGAGCGTGTG 60.110 55.000 0.00 0.00 0.00 3.82
87 88 1.170290 TCGTCAGAGAGCGTGTGGAA 61.170 55.000 0.00 0.00 0.00 3.53
93 94 0.249489 GAGAGCGTGTGGAAGTGTGT 60.249 55.000 0.00 0.00 0.00 3.72
124 135 2.761559 TCTCGCCGATGTTTTTCTTCA 58.238 42.857 0.00 0.00 0.00 3.02
135 146 6.591834 CGATGTTTTTCTTCAGTGGATCTACT 59.408 38.462 5.80 5.80 0.00 2.57
140 151 5.407407 TTCTTCAGTGGATCTACTTGGAC 57.593 43.478 9.32 0.00 0.00 4.02
142 153 2.100197 TCAGTGGATCTACTTGGACCG 58.900 52.381 9.32 0.00 0.00 4.79
144 155 1.006758 AGTGGATCTACTTGGACCGGA 59.993 52.381 9.46 0.00 0.00 5.14
149 160 3.306364 GGATCTACTTGGACCGGATCATG 60.306 52.174 9.46 10.56 35.76 3.07
150 161 3.026707 TCTACTTGGACCGGATCATGA 57.973 47.619 9.46 0.00 0.00 3.07
158 169 2.557056 GGACCGGATCATGATTCGTCTA 59.443 50.000 29.77 0.00 38.11 2.59
163 174 3.550233 CGGATCATGATTCGTCTACGGTT 60.550 47.826 25.46 0.00 40.29 4.44
170 181 5.063180 TGATTCGTCTACGGTTATGTGTT 57.937 39.130 2.24 0.00 40.29 3.32
186 197 4.447138 TGTGTTTACAGGTTGGATCCTT 57.553 40.909 14.23 0.00 35.37 3.36
187 198 4.798882 TGTGTTTACAGGTTGGATCCTTT 58.201 39.130 14.23 0.00 35.37 3.11
189 200 4.825085 GTGTTTACAGGTTGGATCCTTTCA 59.175 41.667 14.23 0.00 35.37 2.69
196 207 4.572389 CAGGTTGGATCCTTTCAATCTACG 59.428 45.833 14.23 0.00 33.10 3.51
197 208 3.312697 GGTTGGATCCTTTCAATCTACGC 59.687 47.826 14.23 0.00 0.00 4.42
209 220 5.582689 TCAATCTACGCTTCTCTTCATCA 57.417 39.130 0.00 0.00 0.00 3.07
211 222 5.126222 TCAATCTACGCTTCTCTTCATCAGT 59.874 40.000 0.00 0.00 0.00 3.41
226 237 3.745975 TCATCAGTGACGATTGTTGTTCC 59.254 43.478 0.00 0.00 0.00 3.62
235 246 1.852067 ATTGTTGTTCCGGTGCGCTC 61.852 55.000 9.73 4.47 0.00 5.03
238 249 4.595538 TGTTCCGGTGCGCTCGTT 62.596 61.111 9.73 0.00 0.00 3.85
266 277 0.526662 CCTTAGCACGACGACTTCCT 59.473 55.000 0.00 0.00 0.00 3.36
275 286 1.400371 CGACGACTTCCTGACTGTCTG 60.400 57.143 9.51 8.50 0.00 3.51
276 287 1.609555 GACGACTTCCTGACTGTCTGT 59.390 52.381 9.51 0.74 0.00 3.41
299 310 2.224818 ACAACAAGGTATGCCCGGTTTA 60.225 45.455 0.00 0.00 38.74 2.01
301 312 1.910671 ACAAGGTATGCCCGGTTTAGA 59.089 47.619 0.00 0.00 38.74 2.10
307 318 3.325716 GGTATGCCCGGTTTAGATAAGGA 59.674 47.826 0.00 0.00 0.00 3.36
322 334 4.324991 GGAAGGGGCGTTGACGGT 62.325 66.667 5.62 0.00 40.23 4.83
334 346 3.047280 GACGGTGGCGTGCATTCA 61.047 61.111 0.00 0.00 0.00 2.57
348 360 0.952497 CATTCAGCACGCTCCAGTGT 60.952 55.000 0.00 0.00 43.61 3.55
361 373 1.677576 TCCAGTGTTTGTAGTCGTCGT 59.322 47.619 0.00 0.00 0.00 4.34
378 390 1.167851 CGTTAGGTGGTCTACGGACA 58.832 55.000 0.00 0.00 43.77 4.02
392 404 2.726821 ACGGACATGGATGCAATTTCT 58.273 42.857 0.00 0.00 0.00 2.52
393 405 3.884895 ACGGACATGGATGCAATTTCTA 58.115 40.909 0.00 0.00 0.00 2.10
408 420 9.691362 ATGCAATTTCTATTACTTTTCGTGTTT 57.309 25.926 0.00 0.00 0.00 2.83
599 613 5.104735 ACAGGCTTAATAAACTGGAGAGAGG 60.105 44.000 8.55 0.00 35.34 3.69
600 614 4.130857 GGCTTAATAAACTGGAGAGAGGC 58.869 47.826 0.00 0.00 0.00 4.70
601 615 4.384208 GGCTTAATAAACTGGAGAGAGGCA 60.384 45.833 0.00 0.00 0.00 4.75
602 616 4.813697 GCTTAATAAACTGGAGAGAGGCAG 59.186 45.833 0.00 0.00 0.00 4.85
603 617 5.395768 GCTTAATAAACTGGAGAGAGGCAGA 60.396 44.000 0.00 0.00 0.00 4.26
604 618 4.751767 AATAAACTGGAGAGAGGCAGAG 57.248 45.455 0.00 0.00 0.00 3.35
605 619 2.317371 AAACTGGAGAGAGGCAGAGA 57.683 50.000 0.00 0.00 0.00 3.10
606 620 1.851304 AACTGGAGAGAGGCAGAGAG 58.149 55.000 0.00 0.00 0.00 3.20
607 621 0.033208 ACTGGAGAGAGGCAGAGAGG 60.033 60.000 0.00 0.00 0.00 3.69
676 690 2.574955 GGCGATGCGATAGTCCCCT 61.575 63.158 0.00 0.00 39.35 4.79
887 907 2.347731 CTTGCCTAGGTCGTTTCTTCC 58.652 52.381 11.31 0.00 0.00 3.46
926 947 2.534903 GGCGGCGATTGGCTTCTAC 61.535 63.158 12.98 0.00 42.94 2.59
1488 1509 1.538629 TGATGTCACTCCCAGGCCA 60.539 57.895 5.01 0.00 0.00 5.36
1548 1569 2.476051 CTGCACCGCGTGATGAAC 59.524 61.111 4.92 0.00 35.23 3.18
1589 1610 2.606519 CGGACCCAAGAGACCCCA 60.607 66.667 0.00 0.00 0.00 4.96
1591 1612 1.846124 GGACCCAAGAGACCCCACA 60.846 63.158 0.00 0.00 0.00 4.17
1612 1633 2.069273 GTATCGCCGATGGGAAAGATG 58.931 52.381 10.41 0.00 36.96 2.90
1613 1634 0.250467 ATCGCCGATGGGAAAGATGG 60.250 55.000 0.00 0.00 36.96 3.51
1614 1635 1.893808 CGCCGATGGGAAAGATGGG 60.894 63.158 0.00 0.00 34.06 4.00
1661 1682 2.028748 GTGATGCTTGCAATGGTTCCTT 60.029 45.455 0.00 0.00 0.00 3.36
1684 1705 0.882927 GCACACGCCAACTGAGGTTA 60.883 55.000 0.00 0.00 33.88 2.85
1722 1743 0.533085 GCTCTGTAGGGAAATCCGGC 60.533 60.000 0.00 0.00 41.52 6.13
1729 1750 1.068250 GGGAAATCCGGCGAGAGAG 59.932 63.158 9.30 0.00 36.71 3.20
1734 1755 1.333177 AATCCGGCGAGAGAGCTATT 58.667 50.000 9.30 0.00 37.29 1.73
1740 1761 1.000717 GGCGAGAGAGCTATTCACTCC 60.001 57.143 0.00 0.00 39.52 3.85
1748 1769 3.704061 AGAGCTATTCACTCCTCCAAGAC 59.296 47.826 0.00 0.00 34.56 3.01
1798 1819 1.691196 TCCTTGGAACACTGCAAAGG 58.309 50.000 4.94 4.94 39.29 3.11
1830 1851 6.449698 GCACATTGTTAATAATGGAGATGGG 58.550 40.000 23.67 4.75 41.29 4.00
1926 1947 5.669477 GGTGAACAGAGAGAAGAGCATAAT 58.331 41.667 0.00 0.00 0.00 1.28
1956 1977 0.043940 AGCAATCCAGAGACCCTCCT 59.956 55.000 0.00 0.00 0.00 3.69
1957 1978 0.179936 GCAATCCAGAGACCCTCCTG 59.820 60.000 0.00 0.00 0.00 3.86
1959 1980 1.209019 CAATCCAGAGACCCTCCTGTG 59.791 57.143 0.00 0.00 0.00 3.66
1960 1981 0.326048 ATCCAGAGACCCTCCTGTGG 60.326 60.000 0.00 0.00 45.86 4.17
1989 2010 2.753452 CTGCAATGAGCTCAAGTCCAAT 59.247 45.455 22.50 0.00 45.94 3.16
1991 2012 2.751259 GCAATGAGCTCAAGTCCAATGA 59.249 45.455 22.50 0.00 41.15 2.57
2003 2024 1.266718 GTCCAATGACGCAGAAAAGCA 59.733 47.619 0.00 0.00 0.00 3.91
2110 2131 0.040425 CAAGAAGTTCAAACCGGCGG 60.040 55.000 27.06 27.06 0.00 6.13
2154 2175 2.096069 CAGCAAGATGTTGTGTTCCTCG 60.096 50.000 4.33 0.00 35.92 4.63
2157 2178 2.086054 AGATGTTGTGTTCCTCGAGC 57.914 50.000 6.99 0.00 0.00 5.03
2160 2181 0.750249 TGTTGTGTTCCTCGAGCTCA 59.250 50.000 15.40 2.59 0.00 4.26
2190 2211 1.743252 CTCTGCTTCCGTGAAGGCC 60.743 63.158 13.33 0.00 39.76 5.19
2191 2212 3.121030 CTGCTTCCGTGAAGGCCG 61.121 66.667 13.33 0.00 39.76 6.13
2192 2213 3.589654 CTGCTTCCGTGAAGGCCGA 62.590 63.158 13.33 0.00 39.76 5.54
2193 2214 2.125106 GCTTCCGTGAAGGCCGAT 60.125 61.111 13.33 0.00 39.76 4.18
2342 2373 3.137459 AGACAGCGAGAGGAGGCG 61.137 66.667 0.00 0.00 0.00 5.52
2352 2383 1.226262 GAGGAGGCGGTCTCTCTCT 59.774 63.158 9.80 0.00 42.10 3.10
2353 2384 0.818040 GAGGAGGCGGTCTCTCTCTC 60.818 65.000 9.80 4.22 42.10 3.20
2354 2385 1.226262 GGAGGCGGTCTCTCTCTCT 59.774 63.158 9.80 0.00 42.10 3.10
2518 2549 9.722056 CAAATTTGCCAGAGTTGATAGTTATAC 57.278 33.333 5.01 0.00 0.00 1.47
2597 2653 3.885297 CCTCTTTGTCTGCCTTTCTTTCA 59.115 43.478 0.00 0.00 0.00 2.69
2599 2655 5.010415 CCTCTTTGTCTGCCTTTCTTTCATT 59.990 40.000 0.00 0.00 0.00 2.57
2608 2664 8.897752 GTCTGCCTTTCTTTCATTCAGTATAAT 58.102 33.333 0.00 0.00 0.00 1.28
2622 2707 6.252599 TCAGTATAATTTCTGGTGGCTGAT 57.747 37.500 0.00 0.00 33.13 2.90
2632 2717 6.499106 TTCTGGTGGCTGATATAAATCTCA 57.501 37.500 0.00 0.00 32.93 3.27
2633 2718 6.499106 TCTGGTGGCTGATATAAATCTCAA 57.501 37.500 0.00 0.00 32.93 3.02
2682 2771 2.477863 GCAACTATGTTCATCCAACCGC 60.478 50.000 0.00 0.00 33.51 5.68
2684 2773 1.559682 ACTATGTTCATCCAACCGCCT 59.440 47.619 0.00 0.00 33.51 5.52
2686 2775 1.923356 ATGTTCATCCAACCGCCTTT 58.077 45.000 0.00 0.00 33.51 3.11
2736 2907 3.123050 GGGCACCGCATTTAAATTCATC 58.877 45.455 0.00 0.00 40.86 2.92
2766 2937 6.215636 ACCTGTTCATTACTCCCTCTGTAAAT 59.784 38.462 0.00 0.00 34.20 1.40
2768 2939 8.265055 CCTGTTCATTACTCCCTCTGTAAATAA 58.735 37.037 0.00 0.00 34.20 1.40
2769 2940 9.667107 CTGTTCATTACTCCCTCTGTAAATAAA 57.333 33.333 0.00 0.00 34.20 1.40
2862 3033 8.792830 TTACAGAGGGAGTACATATAATGGTT 57.207 34.615 0.00 0.00 33.60 3.67
2882 3053 1.756430 CTGATCTCCTCAGGTGACGA 58.244 55.000 0.00 0.00 46.52 4.20
2883 3054 1.403679 CTGATCTCCTCAGGTGACGAC 59.596 57.143 0.00 0.00 46.52 4.34
2965 3136 2.604046 AAATACTCTGTAGCGGCAGG 57.396 50.000 1.45 4.75 37.12 4.85
2995 3166 3.117169 TCCTGGGCAATGGCACTTATATT 60.117 43.478 9.51 0.00 46.28 1.28
3007 3178 5.244851 TGGCACTTATATTTTTGCACCTTGA 59.755 36.000 0.00 0.00 36.66 3.02
3016 3187 4.454728 TTTTGCACCTTGATTATCAGCC 57.545 40.909 0.00 0.00 0.00 4.85
3035 3206 0.179000 CTCAGGCGGTTGAAGGCTAT 59.821 55.000 0.00 0.00 42.91 2.97
3043 3214 0.373716 GTTGAAGGCTATCCGCAACG 59.626 55.000 8.09 0.00 40.20 4.10
3060 3231 3.423206 GCAACGTCTGAAATTCTGCTTTG 59.577 43.478 0.00 2.82 0.00 2.77
3081 3252 2.421399 GGCAAAGATGAGGGCCTGC 61.421 63.158 12.95 7.01 43.09 4.85
3083 3254 2.117156 CAAAGATGAGGGCCTGCCG 61.117 63.158 12.95 0.00 36.85 5.69
3084 3255 3.350031 AAAGATGAGGGCCTGCCGG 62.350 63.158 12.95 0.00 36.85 6.13
3144 3315 5.771469 TGATCAAACAAACATCGATTTGCT 58.229 33.333 10.64 0.00 42.29 3.91
3149 3320 2.256174 CAAACATCGATTTGCTGCCAG 58.744 47.619 0.00 0.00 33.07 4.85
3194 3365 4.254709 AACGCCACAGCCTGCTCA 62.255 61.111 0.00 0.00 34.57 4.26
3195 3366 3.557903 AACGCCACAGCCTGCTCAT 62.558 57.895 0.00 0.00 34.57 2.90
3196 3367 3.200593 CGCCACAGCCTGCTCATC 61.201 66.667 0.00 0.00 34.57 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.148498 CGGGGGTTAGATGGGAAGC 59.852 63.158 0.00 0.00 0.00 3.86
32 33 1.383525 GGACGGGGGTTAGATGGGA 60.384 63.158 0.00 0.00 0.00 4.37
36 37 2.070650 GCCTGGACGGGGGTTAGAT 61.071 63.158 0.00 0.00 0.00 1.98
37 38 2.686106 GCCTGGACGGGGGTTAGA 60.686 66.667 0.00 0.00 0.00 2.10
46 47 3.916392 GAGACACACCGCCTGGACG 62.916 68.421 0.00 0.03 39.21 4.79
51 52 1.293498 GACATGAGACACACCGCCT 59.707 57.895 0.00 0.00 0.00 5.52
59 60 1.470494 GCTCTCTGACGACATGAGACA 59.530 52.381 17.08 0.00 33.82 3.41
87 88 1.203523 GAGATCCGCTGAAGACACACT 59.796 52.381 0.00 0.00 0.00 3.55
101 102 2.280628 AGAAAAACATCGGCGAGATCC 58.719 47.619 17.22 0.58 37.52 3.36
112 123 7.175641 CCAAGTAGATCCACTGAAGAAAAACAT 59.824 37.037 0.00 0.00 0.00 2.71
114 125 6.710744 TCCAAGTAGATCCACTGAAGAAAAAC 59.289 38.462 0.00 0.00 0.00 2.43
124 135 1.006758 TCCGGTCCAAGTAGATCCACT 59.993 52.381 0.00 0.00 0.00 4.00
135 146 1.484653 ACGAATCATGATCCGGTCCAA 59.515 47.619 18.95 0.00 0.00 3.53
140 151 2.585845 CGTAGACGAATCATGATCCGG 58.414 52.381 18.95 8.86 43.02 5.14
142 153 3.644884 ACCGTAGACGAATCATGATCC 57.355 47.619 9.06 0.00 43.02 3.36
144 155 5.920840 CACATAACCGTAGACGAATCATGAT 59.079 40.000 1.18 1.18 43.02 2.45
149 160 6.527722 TGTAAACACATAACCGTAGACGAATC 59.472 38.462 3.07 0.00 43.02 2.52
150 161 6.389091 TGTAAACACATAACCGTAGACGAAT 58.611 36.000 3.07 0.00 43.02 3.34
158 169 3.816523 CCAACCTGTAAACACATAACCGT 59.183 43.478 0.00 0.00 0.00 4.83
163 174 5.772393 AGGATCCAACCTGTAAACACATA 57.228 39.130 15.82 0.00 39.01 2.29
170 181 6.139679 AGATTGAAAGGATCCAACCTGTAA 57.860 37.500 15.82 0.01 40.49 2.41
186 197 5.965922 TGATGAAGAGAAGCGTAGATTGAA 58.034 37.500 0.00 0.00 34.67 2.69
187 198 5.126222 ACTGATGAAGAGAAGCGTAGATTGA 59.874 40.000 0.00 0.00 34.67 2.57
189 200 5.126222 TCACTGATGAAGAGAAGCGTAGATT 59.874 40.000 0.00 0.00 41.04 2.40
196 207 3.223423 TCGTCACTGATGAAGAGAAGC 57.777 47.619 0.00 0.00 38.27 3.86
197 208 5.167121 ACAATCGTCACTGATGAAGAGAAG 58.833 41.667 5.03 0.00 44.94 2.85
209 220 1.202604 ACCGGAACAACAATCGTCACT 60.203 47.619 9.46 0.00 0.00 3.41
211 222 1.222300 CACCGGAACAACAATCGTCA 58.778 50.000 9.46 0.00 0.00 4.35
226 237 4.409588 CAACGAACGAGCGCACCG 62.410 66.667 11.47 15.74 33.86 4.94
235 246 2.396157 GCTAAGGCCCCAACGAACG 61.396 63.158 0.00 0.00 0.00 3.95
238 249 2.349755 GTGCTAAGGCCCCAACGA 59.650 61.111 0.00 0.00 37.74 3.85
240 251 2.038837 GTCGTGCTAAGGCCCCAAC 61.039 63.158 0.00 0.00 37.74 3.77
266 277 4.481368 ACCTTGTTGTAACAGACAGTCA 57.519 40.909 2.66 0.00 39.88 3.41
275 286 1.741145 CCGGGCATACCTTGTTGTAAC 59.259 52.381 0.00 0.00 36.97 2.50
276 287 1.351683 ACCGGGCATACCTTGTTGTAA 59.648 47.619 6.32 0.00 36.97 2.41
299 310 1.209747 GTCAACGCCCCTTCCTTATCT 59.790 52.381 0.00 0.00 0.00 1.98
301 312 0.107848 CGTCAACGCCCCTTCCTTAT 60.108 55.000 0.00 0.00 0.00 1.73
307 318 4.636435 CCACCGTCAACGCCCCTT 62.636 66.667 0.00 0.00 38.18 3.95
334 346 0.105964 TACAAACACTGGAGCGTGCT 59.894 50.000 0.00 0.00 38.45 4.40
337 349 1.602165 CGACTACAAACACTGGAGCGT 60.602 52.381 0.00 0.00 40.05 5.07
348 360 2.622942 ACCACCTAACGACGACTACAAA 59.377 45.455 0.00 0.00 0.00 2.83
361 373 2.104967 CCATGTCCGTAGACCACCTAA 58.895 52.381 0.00 0.00 42.81 2.69
378 390 8.686334 ACGAAAAGTAATAGAAATTGCATCCAT 58.314 29.630 0.00 0.00 30.73 3.41
495 509 1.202604 ACAAACAGTGGTAGTCGTGGG 60.203 52.381 0.00 0.00 0.00 4.61
500 514 5.924825 CCAGTAAGTACAAACAGTGGTAGTC 59.075 44.000 0.00 0.00 0.00 2.59
599 613 1.381056 TCCCTCTCTGCCTCTCTGC 60.381 63.158 0.00 0.00 0.00 4.26
600 614 0.258484 TCTCCCTCTCTGCCTCTCTG 59.742 60.000 0.00 0.00 0.00 3.35
601 615 0.552848 CTCTCCCTCTCTGCCTCTCT 59.447 60.000 0.00 0.00 0.00 3.10
602 616 0.550914 TCTCTCCCTCTCTGCCTCTC 59.449 60.000 0.00 0.00 0.00 3.20
603 617 0.552848 CTCTCTCCCTCTCTGCCTCT 59.447 60.000 0.00 0.00 0.00 3.69
604 618 0.550914 TCTCTCTCCCTCTCTGCCTC 59.449 60.000 0.00 0.00 0.00 4.70
605 619 0.552848 CTCTCTCTCCCTCTCTGCCT 59.447 60.000 0.00 0.00 0.00 4.75
606 620 0.550914 TCTCTCTCTCCCTCTCTGCC 59.449 60.000 0.00 0.00 0.00 4.85
607 621 1.680338 GTCTCTCTCTCCCTCTCTGC 58.320 60.000 0.00 0.00 0.00 4.26
676 690 3.948719 GCGGTGGTGGAGGTGGAA 61.949 66.667 0.00 0.00 0.00 3.53
869 889 1.549170 GAGGAAGAAACGACCTAGGCA 59.451 52.381 9.30 0.00 33.89 4.75
887 907 1.300465 CGCTGGACGGATGGATGAG 60.300 63.158 0.00 0.00 38.44 2.90
909 930 2.534903 GGTAGAAGCCAATCGCCGC 61.535 63.158 0.00 0.00 38.78 6.53
921 942 2.166459 CGAGATTCACTGCCAGGTAGAA 59.834 50.000 12.26 0.00 0.00 2.10
926 947 1.088340 CAGCGAGATTCACTGCCAGG 61.088 60.000 0.00 0.00 0.00 4.45
946 967 0.042708 CGGATCTGCGCAGAAATTCG 60.043 55.000 40.83 31.43 41.36 3.34
1548 1569 2.897350 GAAATCCGGGGCGAGCTG 60.897 66.667 0.00 0.00 0.00 4.24
1589 1610 0.828022 TTTCCCATCGGCGATACTGT 59.172 50.000 23.53 0.00 0.00 3.55
1591 1612 1.410004 TCTTTCCCATCGGCGATACT 58.590 50.000 23.53 0.00 0.00 2.12
1684 1705 2.036862 AGCTTCCTCCGTTAACGAAACT 59.963 45.455 28.79 12.57 43.02 2.66
1722 1743 2.552315 GGAGGAGTGAATAGCTCTCTCG 59.448 54.545 0.00 0.00 42.99 4.04
1729 1750 4.038642 CCTAGTCTTGGAGGAGTGAATAGC 59.961 50.000 0.00 0.00 34.46 2.97
1734 1755 1.619977 GCCCTAGTCTTGGAGGAGTGA 60.620 57.143 1.39 0.00 34.46 3.41
1740 1761 1.395826 CCGGAGCCCTAGTCTTGGAG 61.396 65.000 0.00 0.00 0.00 3.86
1748 1769 3.584052 CGTCGTCCGGAGCCCTAG 61.584 72.222 3.06 0.00 0.00 3.02
1798 1819 0.602562 TTAACAATGTGCCTGCTGCC 59.397 50.000 0.00 0.00 40.16 4.85
1830 1851 1.401905 CCAGCGCTTAGGTTTCCAATC 59.598 52.381 7.50 0.00 0.00 2.67
1926 1947 4.040829 TCTCTGGATTGCTCTGTTTCTTGA 59.959 41.667 0.00 0.00 0.00 3.02
1956 1977 2.171237 CTCATTGCAGTATCCTCCCACA 59.829 50.000 0.00 0.00 0.00 4.17
1957 1978 2.843701 CTCATTGCAGTATCCTCCCAC 58.156 52.381 0.00 0.00 0.00 4.61
1959 1980 1.419387 AGCTCATTGCAGTATCCTCCC 59.581 52.381 0.00 0.00 45.94 4.30
1960 1981 2.103771 TGAGCTCATTGCAGTATCCTCC 59.896 50.000 13.74 0.00 45.94 4.30
1961 1982 3.465742 TGAGCTCATTGCAGTATCCTC 57.534 47.619 13.74 0.00 45.94 3.71
1989 2010 0.662619 CAGGTTGCTTTTCTGCGTCA 59.337 50.000 0.00 0.00 35.36 4.35
1991 2012 0.751643 ACCAGGTTGCTTTTCTGCGT 60.752 50.000 0.00 0.00 35.36 5.24
2003 2024 1.444250 TCGTCTGCGAAACCAGGTT 59.556 52.632 0.00 0.00 44.92 3.50
2046 2067 4.545706 GGCGCGGGATCATCACCA 62.546 66.667 8.83 0.00 0.00 4.17
2049 2070 4.585526 GTCGGCGCGGGATCATCA 62.586 66.667 15.48 0.00 0.00 3.07
2154 2175 2.394563 GGTTTCAGCCGCTGAGCTC 61.395 63.158 21.87 15.49 42.61 4.09
2157 2178 1.294780 AGAGGTTTCAGCCGCTGAG 59.705 57.895 21.87 0.00 41.75 3.35
2160 2181 2.359230 GCAGAGGTTTCAGCCGCT 60.359 61.111 0.00 0.00 39.26 5.52
2190 2211 4.392921 ACCTCACCTCACTAATCAATCG 57.607 45.455 0.00 0.00 0.00 3.34
2191 2212 5.491982 ACAACCTCACCTCACTAATCAATC 58.508 41.667 0.00 0.00 0.00 2.67
2192 2213 5.505181 ACAACCTCACCTCACTAATCAAT 57.495 39.130 0.00 0.00 0.00 2.57
2193 2214 4.974645 ACAACCTCACCTCACTAATCAA 57.025 40.909 0.00 0.00 0.00 2.57
2244 2273 1.068281 AGCTAGGACACGCATCTGATG 59.932 52.381 13.26 13.26 0.00 3.07
2245 2274 1.407936 AGCTAGGACACGCATCTGAT 58.592 50.000 0.00 0.00 0.00 2.90
2342 2373 4.583073 GGAATCTACCAAGAGAGAGAGACC 59.417 50.000 0.00 0.00 34.49 3.85
2352 2383 3.913799 TGAAAGGTGGGAATCTACCAAGA 59.086 43.478 9.21 0.00 45.75 3.02
2353 2384 4.301072 TGAAAGGTGGGAATCTACCAAG 57.699 45.455 9.21 0.00 45.75 3.61
2354 2385 4.946160 ATGAAAGGTGGGAATCTACCAA 57.054 40.909 9.21 0.00 45.75 3.67
2518 2549 4.314961 TCACCAAGCAGTACAACATGTAG 58.685 43.478 0.00 0.00 32.84 2.74
2597 2653 6.662755 TCAGCCACCAGAAATTATACTGAAT 58.337 36.000 0.00 0.00 36.38 2.57
2599 2655 5.692115 TCAGCCACCAGAAATTATACTGA 57.308 39.130 0.00 0.00 36.38 3.41
2608 2664 6.899089 TGAGATTTATATCAGCCACCAGAAA 58.101 36.000 0.00 0.00 32.95 2.52
2611 2667 7.756395 AATTGAGATTTATATCAGCCACCAG 57.244 36.000 0.00 0.00 32.95 4.00
2612 2668 9.812347 ATAAATTGAGATTTATATCAGCCACCA 57.188 29.630 3.29 0.00 43.34 4.17
2632 2717 9.429359 CGCTAGGAGTCATATTCAGAATAAATT 57.571 33.333 6.96 0.00 0.00 1.82
2633 2718 7.547370 GCGCTAGGAGTCATATTCAGAATAAAT 59.453 37.037 6.96 0.00 0.00 1.40
2646 2731 0.460987 GTTGCTGCGCTAGGAGTCAT 60.461 55.000 9.73 0.00 38.17 3.06
2672 2761 2.929398 GCAATTAAAAGGCGGTTGGATG 59.071 45.455 0.00 0.00 0.00 3.51
2682 2771 9.565213 TCAAACAAAAATGTTGCAATTAAAAGG 57.435 25.926 0.59 0.00 31.64 3.11
2736 2907 7.070074 ACAGAGGGAGTAATGAACAGGTTATAG 59.930 40.741 0.00 0.00 0.00 1.31
2881 3052 3.412386 AGTCCTGTTGGCTTAATGTGTC 58.588 45.455 0.00 0.00 0.00 3.67
2882 3053 3.181445 TGAGTCCTGTTGGCTTAATGTGT 60.181 43.478 0.00 0.00 0.00 3.72
2883 3054 3.411446 TGAGTCCTGTTGGCTTAATGTG 58.589 45.455 0.00 0.00 0.00 3.21
2965 3136 1.891150 CCATTGCCCAGGATATCAAGC 59.109 52.381 4.83 2.08 0.00 4.01
2979 3150 5.220643 GGTGCAAAAATATAAGTGCCATTGC 60.221 40.000 0.00 0.00 41.56 3.56
2995 3166 4.088634 AGGCTGATAATCAAGGTGCAAAA 58.911 39.130 0.00 0.00 0.00 2.44
3014 3185 2.747855 CCTTCAACCGCCTGAGGC 60.748 66.667 14.89 14.89 46.75 4.70
3016 3187 0.179000 ATAGCCTTCAACCGCCTGAG 59.821 55.000 0.00 0.00 0.00 3.35
3035 3206 1.798223 CAGAATTTCAGACGTTGCGGA 59.202 47.619 0.00 0.00 0.00 5.54
3043 3214 3.737774 GCCAACAAAGCAGAATTTCAGAC 59.262 43.478 0.00 0.00 0.00 3.51
3060 3231 0.613012 AGGCCCTCATCTTTGCCAAC 60.613 55.000 0.00 0.00 46.45 3.77
3091 3262 1.615116 CCCAGAAATGGCTGAAGCTCA 60.615 52.381 1.74 0.00 41.70 4.26
3115 3286 7.806409 ATCGATGTTTGTTTGATCATATCCA 57.194 32.000 0.00 0.00 0.00 3.41
3144 3315 0.844661 ATCAGGGGGTGTTACTGGCA 60.845 55.000 0.00 0.00 33.19 4.92
3149 3320 1.810412 GCGATCATCAGGGGGTGTTAC 60.810 57.143 0.00 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.