Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011227.1 Kokia drynarioides strain JFW-HI SEQ_126205, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 85611
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:4665 original size:8 final size:8
Alignment explanation
Indices: 4652--4681 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
4642 AATTTCACCC
4652 AAAAAAAT
1 AAAAAAAT
4660 AAAAAAAT
1 AAAAAAAT
4668 -AAAAAAT
1 AAAAAAAT
4675 AAAAAAA
1 AAAAAAA
4682 GGAAGAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:4671 original size:15 final size:15
Alignment explanation
Indices: 4653--4681 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4643 ATTTCACCCA
4653 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
4668 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
4682 GGAAGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:4693 original size:15 final size:15
Alignment explanation
Indices: 4675--4717 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
4665 AATAAAAAAT
4675 AAAAAAAGGAAGAGAA
1 AAAAAAAGGAA-AGAA
*
4691 AAAAAAAAGAAAGAA
1 AAAAAAAGGAAAGAA
*
4706 AAAATAAGGAAA
1 AAAAAAAGGAAA
4718 AAGAAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (15 bp):
AAAAAAAGGAAAGAA
Found at i:4729 original size:40 final size:37
Alignment explanation
Indices: 4652--4723 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
4642 AATTTCACCC
* *
4652 AAAAAAATAAAAAAATAAAAAATAAAAAAAGGAAGAG
1 AAAAAAATAAAAAAAGAAAAAATAAAAAAAGAAAGAG
*
4689 AAAAAAA-AAAGAAAGAAAAAATAAGGAAAAAGAAA
1 AAAAAAATAAAAAAAGAAAAAATAA--AAAAAGAAA
4724 AAGAGAGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 15 0.50
37 7 0.23
38 8 0.27
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (37 bp):
AAAAAAATAAAAAAAGAAAAAATAAAAAAAGAAAGAG
Found at i:5245 original size:105 final size:105
Alignment explanation
Indices: 5026--5294 Score: 416
Period size: 105 Copynumber: 2.6 Consensus size: 105
5016 TCATATGCAT
** * *
5026 GAGCTTTGCCTCTTATAAAATTAAATTTTATCCATCTTACAACCCTATTCAAGCA-TTTTTGCAA
1 GAGCTTTGCCTCCAATAAAATTCAATTTTATCCATCTTACAACCCTGTTCAAGCATTTTTTGCAA
*
5090 CAGTTAGTGGACTAATGATTTTTAATCTTTTAATTCATGC
66 CAGTTAGTGGACTAATGATTTTTAATATTTTAATTCATGC
* *
5130 GAGTTTTGCCTCCAATAAAATTCAATTTTATTCATCTTACAACCCTGTTCAAGCATTTTTTGCAA
1 GAGCTTTGCCTCCAATAAAATTCAATTTTATCCATCTTACAACCCTGTTCAAGCATTTTTTGCAA
*
5195 C-GATTAGTGGACTAATGATTTTTAATATTTTCATTCATGC
66 CAG-TTAGTGGACTAATGATTTTTAATATTTTAATTCATGC
* * *
5235 GAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAATCTTGTTCAAGCATTTTT
1 GAGCTTTGCCTCCAATAAAATTCAATTTTATCCATCTTACAACCCTGTTCAAGCATTTTT
5295 GCATTAAAAT
Statistics
Matches: 150, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
104 50 0.33
105 100 0.67
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.41
Consensus pattern (105 bp):
GAGCTTTGCCTCCAATAAAATTCAATTTTATCCATCTTACAACCCTGTTCAAGCATTTTTTGCAA
CAGTTAGTGGACTAATGATTTTTAATATTTTAATTCATGC
Found at i:5914 original size:42 final size:44
Alignment explanation
Indices: 5820--5936 Score: 129
Period size: 42 Copynumber: 2.8 Consensus size: 44
5810 GAAGATGAGG
* *
5820 AGAAG-TAGATTGAAGCCGCAAAGACAAATCTC-AAGACATTAG
1 AGAAGCTAGATTGAAGCCGCAAAGGCAAATCTCAAAGACATTAA
5862 AGAAGC-AGATTGAAGCCGCAAAGGCAAATCTCAAAG-C-TTCAA
1 AGAAGCTAGATTGAAGCCGCAAAGGCAAATCTCAAAGACATT-AA
* ** *
5904 AG-GGCTAGATTGAAGTTGCAAAGGCGAATCTCA
1 AGAAGCTAGATTGAAGCCGCAAAGGCAAATCTCA
5937 CGTCCTTAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
41 4 0.06
42 58 0.89
43 3 0.05
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (44 bp):
AGAAGCTAGATTGAAGCCGCAAAGGCAAATCTCAAAGACATTAA
Found at i:6144 original size:94 final size:93
Alignment explanation
Indices: 6028--6536 Score: 413
Period size: 94 Copynumber: 5.4 Consensus size: 93
6018 GAACAAAGTG
* *
6028 GATCTCAATGTCCCTGAGGTTACAATGGAGTGGTGTGAAGCACCAGAATCCTATACCCCTGAGTT
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACCA-AATCCTATACCCCTGAGTT
* * *
6093 GCAGTGGGTCGGATAAAAATAAAGAAGCA
65 ACAGTGGGTCGGATTAAAATAAGGAAGCA
* * * * *
6122 GAGCTCAACGTCCCTGAAGTTACAGTGGAGTGGAGTG-AG-ACTTCAAATCCCAT-CTTCCTGGT
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCAC--CAAATCCTATAC--CC--CT
* * * * * * *
6184 GAGGTACAGAGAAGTGGGA-TAAAA-CAGGTAGTA
60 GAGTTACAGTG-GGTCGGATTAAAATAAGGAAGCA
* * *
6217 GATCTCAGCGTCCCTGAGGTTATAATGGTGTGGAGTGAAGCACCATAATCCTATACCCCTGAGTT
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACCA-AATCCTATACCCCTGAGTT
* * *
6282 ACAGTGGGTCGGATGAAAATAATGAAGTA
65 ACAGTGGGTCGGATTAAAATAAGGAAGCA
* * * ** *
6311 GATCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAAACTTCAAATCCTAT-CTTCCTGGTGA
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACCAAATCCTATAC--CC--CTGA
* * * * *
6375 GGTACAGAGAAG-CGGGTTAAAAT-AGGTAGCA
62 GTTACAGTG-GGTCGGATTAAAATAAGGAAGCA
* * *
6406 GATCTCAACGTCCTTAAGGTTACAATGGAGTGGAGTGAAGCACCAAAATCCTATACCCCTAAGTT
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACC-AAATCCTATACCCCTGAGTT
* * *
6471 GCAGTGGGTCAGATTAAAATAATGAAGCA
65 ACAGTGGGTCGGATTAAAATAAGGAAGCA
* * ** * *
6500 GAGCTTAAAATCTCTGAGGTTACAGTGGAGTGGAGTG
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTG
6537 GAGTGAAACT
Statistics
Matches: 320, Mismatches: 73, Indels: 44
0.73 0.17 0.10
Matches are distributed among these distances:
92 10 0.03
93 48 0.15
94 116 0.36
95 86 0.27
96 50 0.16
97 10 0.03
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (93 bp):
GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACCAAATCCTATACCCCTGAGTTA
CAGTGGGTCGGATTAAAATAAGGAAGCA
Found at i:6251 original size:95 final size:95
Alignment explanation
Indices: 6118--6828 Score: 559
Period size: 95 Copynumber: 7.4 Consensus size: 95
6108 AAAATAAAGA
* *
6118 AGCAGAGCTCAACGTCCCTGAAGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGG
1 AGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGG
6183 TGAGGTACAGAGAAGTGGGATAAAACAGGT
66 TGAGGTACAGAGAAGTGGGATAAAACAGGT
* * * * * *
6213 AGTAGATCTCAGCGTCCCTGAGGTTATAATGGTGTGGAGTGAAGCAC--CATAATCCTATAC--C
1 AGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTG-AG-ACTTCA-AATCCCAT-CTTC
* * * * * * * *
6274 C--CTGAGTTACAGTG-GGTCGGATGAAAATAATGA
62 CTGGTGAGGTACAGAGAAGTGGGAT-AAAA-CAGGT
* * * *
6307 AGTAGATCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAAACTTCAAATCCTATCTTCCTGG
1 AGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGG
* * *
6372 TGAGGTACAGAGAAGCGGGTTAAAATAGGT
66 TGAGGTACAGAGAAGTGGGATAAAACAGGT
* * * *
6402 AGCAGATCTCAACGTCCTTAAGGTTACAATGGAGTGGAGTGAAGCAC--CAAAATCCTATAC--C
1 AGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTG-AG-ACTTC-AAATCCCAT-CTTC
* * * * * * ** * * *
6463 C--CTAAGTTGCAGTG-GGTCAGATTAAAATAATGA
62 CTGGTGAGGTACAGAGAAGTGGGA-TAAAA-CAGGT
* * ** * *
6496 AGCAGAGCTTAAAATCTCTGAGGTTACAGTGGAGTGGAGTGGAGTGAAACTTCAAATCCGATCTT
1 AGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGT-GA--G--ACTTCAAATCCCATCTT
* * * * *
6561 CTTGGTGAGGTATAGAGAACTAGGTTAAAACAGGT
61 CCTGGTGAGGTACAGAGAAGTGGGATAAAACAGGT
* * * * *
6596 AACAGATCTCAATGTCCCTGAGGTTATAGTTGGACTGGAGTGAGATTTCAAATCCCATCTTCCTG
1 AGCAGATCTCAACGTCCCTGAGGTTACAG-TGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTG
* *
6661 GTGAGGTACAGAGAAATGGGATAAAATAGGT
65 GTGAGGTACAGAGAAGTGGGATAAAACAGGT
* * * * *
6692 AGCAAATCTCAACTTCCCTGAGGTTACAGTGGAGAGGAGTGAGTCTTCAAGTCCCATCTTCCTGG
1 AGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGG
* * *
6757 TGAGGTACAGAGAAGTAGGTTAAAACAAGT
66 TGAGGTACAGAGAAGTGGGATAAAACAGGT
* * *
6787 AGCAGATCTCAACATCCTTGAGATTACAGTGGAGTGGAGTGA
1 AGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGA
6829 AGCACCAGAT
Statistics
Matches: 475, Mismatches: 110, Indels: 62
0.73 0.17 0.10
Matches are distributed among these distances:
92 11 0.02
93 36 0.08
94 77 0.16
95 175 0.37
96 102 0.21
97 13 0.03
98 9 0.02
99 2 0.00
100 26 0.05
101 22 0.05
102 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (95 bp):
AGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGG
TGAGGTACAGAGAAGTGGGATAAAACAGGT
Found at i:6348 original size:189 final size:187
Alignment explanation
Indices: 6028--6844 Score: 904
Period size: 189 Copynumber: 4.3 Consensus size: 187
6018 GAACAAAGTG
* *
6028 GATCTCAATGTCCCTGAGGTTACAATGGAGTGGTGTGAAGCACCAGAATCCTATACCCCTGAGTT
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACCA-AATCCTATACCCCTGAGTT
* * *
6093 GCAGTGGGTCGGATAAAAATAAAGAAGCAGAGCTCAACGTCCCTGAAGTTACAGTGGAGTGGAGT
65 ACAGTGGGTCGGAT-AAAATAATGAAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGT
* * *
6158 GAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTGGGATAAAACAGGTAGTA
129 GAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTTAAAACAGGTAGCA
* * *
6217 GATCTCAGCGTCCCTGAGGTTATAATGGTGTGGAGTGAAGCACCATAATCCTATACCCCTGAGTT
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACCA-AATCCTATACCCCTGAGTT
* * *
6282 ACAGTGGGTCGGATGAAAATAATGAAGTAGATCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGT
65 ACAGTGGGTCGGAT-AAAATAATGAAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGT
* * ** *
6347 GAAACTTCAAATCCTATCTTCCTGGTGAGGTACAGAGAAGCGGGTTAAAATAGGTAGCA
129 GAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTTAAAACAGGTAGCA
* * *
6406 GATCTCAACGTCCTTAAGGTTACAATGGAGTGGAGTGAAGCACCAAAATCCTATACCCCTAAGTT
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACC-AAATCCTATACCCCTGAGTT
* * * ** *
6471 GCAGTGGGTCAGATTAAAATAATGAAGCAGAGCTTAAAATCTCTGAGGTTACAGTGGAGTGGAGT
65 ACAGTGGGTCGGA-TAAAATAATGAAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGT
* * * * *
6536 GGAGTGAAACTTCAAATCCGATCTTCTTGGTGAGGTATAGAGAACTAGGTTAAAACAGGTAACA
129 -GA--G--ACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTTAAAACAGGTAGCA
* * * * * * *
6600 GATCTCAATGTCCCTGAGGTTATAGTTGGACTGGAGTG-AG-ATTTCAAATCCCAT-CTTCCTGG
1 GATCTCAACGTCCCTGAGGTTACA-ATGGAGTGGAGTGAAGCA--CCAAATCCTATAC--CC--C
* * ** * * * * * *
6662 TGAGGTACAGAGAAATGGGATAAAAT-AGGTAGCAAATCTCAACTTCCCTGAGGTTACAGTGGAG
59 TGAGTTACAGTG-GGTCGGATAAAATAATGAAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAG
* * * *
6726 AGGAGTGAGTCTTCAAGTCCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTTAAAACAAGTAGCA
123 TGGAGTGAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTTAAAACAGGTAGCA
* * * * *
6791 GATCTCAACATCCTTGAGATTACAGTGGAGTGGAGTGAAGCACCAGATCCTATA
1 GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACCAAATCCTATA
6845 TCCTTGAAGT
Statistics
Matches: 523, Mismatches: 87, Indels: 34
0.81 0.14 0.05
Matches are distributed among these distances:
189 281 0.54
190 23 0.04
191 69 0.13
192 1 0.00
193 3 0.01
194 78 0.15
195 16 0.03
196 35 0.07
197 14 0.03
198 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (187 bp):
GATCTCAACGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCACCAAATCCTATACCCCTGAGTTA
CAGTGGGTCGGATAAAATAATGAAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGA
GACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTTAAAACAGGTAGCA
Found at i:6822 original size:385 final size:378
Alignment explanation
Indices: 6028--6875 Score: 999
Period size: 385 Copynumber: 2.2 Consensus size: 378
6018 GAACAAAGTG
* * * * *
6028 GATCTCAATGTCCCTGAGGTTACAATGGAGTGGTGTGAAGCACCAGAATCCTATACCCCTGAGTT
1 GATCTCAACGTCCTTGAGGTTACAATGGAGTGGAGTGAAGCACCAAAATCCTATACCCCTAAGTT
* **
6093 GCAGTGGGTCGGATAAAAATAAAGAAGCAGAGCTCAACGTCCCTGAAGTTACAGTGGAGTGGAGT
66 GCAGTGGGTCAGATAAAAATAAAGAAGCAGAGCTCAAAATCCCTGAAGTTACAGTGGAGTGGAGT
* * **
6158 GAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGTGGGATAAAACAGGTAGTAGATCTC
131 GAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAACTAGGATAAAACAGGTAACAGATCTC
* ** * * *
6223 AGCGTCCCTGAGGTTATAATGGTGTGGAGTGAAGCACCATAATCCTATACCCCTGAGTTACAGTG
196 AACGTCCCTGAGGTTATAATGGACTGGAGTGAAGCACCATAATCCCATACCCCTGAGGTACAGAG
** * * * * *
6288 GGTCGGATGAAAATAATGAAGTAGATCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAAACT
261 AATCGGATGAAAATAAGGAAGCAAATCTCAACGTCCCTGAGGTTACAGTGGAGAGGAGTGAAACT
* * * *
6353 TCAAATCCTATCTTCCTGGTGAGGTACAGAGAAGCGGGTTAAAATAGGTAGCA
326 TCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGCAGGTTAAAACAAGTAGCA
*
6406 GATCTCAACGTCCTTAAGGTTACAATGGAGTGGAGTGAAGCACCAAAATCCTATACCCCTAAGTT
1 GATCTCAACGTCCTTGAGGTTACAATGGAGTGGAGTGAAGCACCAAAATCCTATACCCCTAAGTT
* * * * *
6471 GCAGTGGGTCAGATTAAAATAATGAAGCAGAGCTTAAAATCTCTGAGGTTACAGTGGAGTGGAGT
66 GCAGTGGGTCAGATAAAAATAAAGAAGCAGAGCTCAAAATCCCTGAAGTTACAGTGGAGTGGAGT
* * * *
6536 GGAGTGAAACTTCAAATCCGATCTTCTTGGTGAGGTATAGAGAACTAGGTTAAAACAGGTAACAG
131 -GA--G--ACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAACTAGGATAAAACAGGTAACAG
* * * *
6601 ATCTCAATGTCCCTGAGGTTATAGTTGGACTGGAGTG-AG-ATTTCA-AATCCCAT-CTTCCTGG
191 ATCTCAACGTCCCTGAGGTTATA-ATGGACTGGAGTGAAGCA--CCATAATCCCATAC--CC--C
* * *
6662 TGAGGTACAGAGAAATGGGAT-AAAAT-AGGTAGCAAATCTCAACTTCCCTGAGGTTACAGTGGA
249 TGAGGTACAGAG-AATCGGATGAAAATAAGGAAGCAAATCTCAACGTCCCTGAGGTTACAGTGGA
** * *
6725 GAGGAGTGAGTCTTCAAGTCCCATCTTCCTGGTGAGGTACAGAGAAGTAGGTTAAAACAAGTAGC
313 GAGGAGTGAAACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGCAGGTTAAAACAAGTAGC
6790 A
378 A
* * * * * *
6791 GATCTCAACATCCTTGAGATTACAGTGGAGTGGAGTGAAGCACC-AGATCCTATATCCTTGAAGT
1 GATCTCAACGTCCTTGAGGTTACAATGGAGTGGAGTGAAGCACCAAAATCCTATACCCCT-AAGT
* *
6855 AGCAGTGGATCAGATAAAAAT
65 TGCAGTGGGTCAGATAAAAAT
6876 GAGTAATGAA
Statistics
Matches: 396, Mismatches: 60, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
378 116 0.29
379 2 0.01
381 1 0.00
382 2 0.01
383 79 0.20
384 26 0.07
385 150 0.38
386 15 0.04
387 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.25
Consensus pattern (378 bp):
GATCTCAACGTCCTTGAGGTTACAATGGAGTGGAGTGAAGCACCAAAATCCTATACCCCTAAGTT
GCAGTGGGTCAGATAAAAATAAAGAAGCAGAGCTCAAAATCCCTGAAGTTACAGTGGAGTGGAGT
GAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAACTAGGATAAAACAGGTAACAGATCTC
AACGTCCCTGAGGTTATAATGGACTGGAGTGAAGCACCATAATCCCATACCCCTGAGGTACAGAG
AATCGGATGAAAATAAGGAAGCAAATCTCAACGTCCCTGAGGTTACAGTGGAGAGGAGTGAAACT
TCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGCAGGTTAAAACAAGTAGCA
Found at i:6994 original size:45 final size:45
Alignment explanation
Indices: 6930--7371 Score: 463
Period size: 45 Copynumber: 10.0 Consensus size: 45
6920 GAAGTTACAT
* **
6930 CACCATCCAATCTTCTACCCCTAGTCAAGAGGGGTAGAACGAAGC
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTGAAGC
* *
6975 CACCATCCAATCTTTTACCCCTAAGTAAAGAGGGGTAGATTGAAGT
1 CACCATCCAATCTTTTACCCCT-AGTCAAGAGGGGTAGATTGAAGC
* *
7021 CACCATCCAATC-TTTACCCCTAGTCAAGAGGGCT-GATTAAAGC
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTGAAGC
* * *
7064 CACCATCCAATCTTTTACCGCTAAGTCAAGAGGGGCAGATTGAAGT
1 CACCATCCAATCTTTTACCCCT-AGTCAAGAGGGGTAGATTGAAGC
* * *
7110 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGAAAATTAAAGC
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTGAAGC
* *
7155 CACCATTCAATCTTTTACCCCTAGTCAAGAAGGGTAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTGAAGC
* * * * * *
7200 CATCGTCAAATCTTTTA-CCCTAGTCAAGAAGGGTAAATTGAATC
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTGAAGC
* * * * *
7244 CACCGTTCAATCTTTTACCTCTACTCAAGAGGGGCAGATTGAAG-
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTGAAGC
* * * * * * *
7288 --TCATCCAGTCTTTTACCGCTAATCTAGAGGGGTAGGTTAAAG-
1 CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTGAAGC
* * *
7330 CA--ATCCAATCTTTTA-ACCTTGATCTAGAGGGGTAGATTGAAG
1 CACCATCCAATCTTTTACCCCTAG-TCAAGAGGGGTAGATTGAAG
7372 TCACACACAC
Statistics
Matches: 333, Mismatches: 56, Indels: 19
0.82 0.14 0.05
Matches are distributed among these distances:
41 2 0.01
42 62 0.19
43 19 0.06
44 58 0.17
45 133 0.40
46 59 0.18
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTGAAGC
Found at i:7082 original size:89 final size:90
Alignment explanation
Indices: 6929--7375 Score: 500
Period size: 89 Copynumber: 5.0 Consensus size: 90
6919 TGAAGTTACA
* ***
6929 TCACCATCCAATCTTCTACCCCTAGTCAAGAGGGGTAGAACGAAGCCACCATCCAATCTTTTACC
1 TCACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTAAAGCCACCATCCAATCTTTTACC
*
6994 CCTAAGTAAAGAGGGGTAGATTGAAG
66 CCT-AGTCAAGAGGGGTAGATTGAAG
*
7020 TCACCATCCAATC-TTTACCCCTAGTCAAGAGGGCT-GATTAAAGCCACCATCCAATCTTTTACC
1 TCACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTAAAGCCACCATCCAATCTTTTACC
* *
7083 GCTAAGTCAAGAGGGGCAGATTGAAG
66 CCT-AGTCAAGAGGGGTAGATTGAAG
* * *
7109 TCACCATCCAATCTTTTACCCCTAGTCAAGAGGGGAAAATTAAAGCCACCATTCAATCTTTTACC
1 TCACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTAAAGCCACCATCCAATCTTTTACC
*
7174 CCTAGTCAAGAAGGGTAGATTGAAG
66 CCTAGTCAAGAGGGGTAGATTGAAG
* * * * * * * * * *
7199 CCATCGTCAAATCTTTTA-CCCTAGTCAAGAAGGGTAAATTGAATCCACCGTTCAATCTTTTACC
1 TCACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTAAAGCCACCATCCAATCTTTTACC
* * *
7263 TCTACTCAAGAGGGGCAGATTGAAG
66 CCTAGTCAAGAGGGGTAGATTGAAG
* * * * * *
7288 T---CATCCAGTCTTTTACCGCTAATCTAGAGGGGTAGGTTAAAG-CA--ATCCAATCTTTTA-A
1 TCACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTAAAGCCACCATCCAATCTTTTACC
* *
7346 CCTTGATCTAGAGGGGTAGATTGAAG
66 CCTAG-TCAAGAGGGGTAGATTGAAG
7372 TCAC
1 TCAC
7376 ACACACAACT
Statistics
Matches: 301, Mismatches: 48, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
83 2 0.01
84 30 0.10
86 13 0.04
87 18 0.06
89 123 0.41
90 74 0.25
91 41 0.14
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (90 bp):
TCACCATCCAATCTTTTACCCCTAGTCAAGAGGGGTAGATTAAAGCCACCATCCAATCTTTTACC
CCTAGTCAAGAGGGGTAGATTGAAG
Found at i:7728 original size:3 final size:3
Alignment explanation
Indices: 7720--7747 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
7710 AAACAAAACA
7720 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
7748 TTAAAAGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:7856 original size:9 final size:9
Alignment explanation
Indices: 7842--7868 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
7832 ATTGCCTAAG
7842 GGCCCAAAT
1 GGCCCAAAT
7851 GGCCCAAAT
1 GGCCCAAAT
7860 GGCCCAAAT
1 GGCCCAAAT
7869 CCAAAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (9 bp):
GGCCCAAAT
Found at i:9377 original size:25 final size:26
Alignment explanation
Indices: 9315--9395 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 26
9305 AATTTGCCCT
* *
9315 TTTTATTCTATTTCTTAAAATTAAATCC
1 TTTTATTCAATTT-TT-AAATTAAACCC
*
9343 TTTTATT---TTTTT--ATT-AATCC
1 TTTTATTCAATTTTTAAATTAAACCC
9363 TTTTATTCAATTTTTAAATTAAACCC
1 TTTTATTCAATTTTTAAATTAAACCC
9389 TTTTATT
1 TTTTATT
9396 TTAAAATTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
20 12 0.26
21 3 0.07
23 5 0.11
24 2 0.04
25 6 0.13
26 11 0.24
28 7 0.15
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTATTCAATTTTTAAATTAAACCC
Found at i:9402 original size:21 final size:21
Alignment explanation
Indices: 9372--9418 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
9362 CTTTTATTCA
*
9372 ATTTTTAAATTAAACCCTTTT
1 ATTTTAAAATTAAACCCTTTT
* **
9393 ATTTTAAAATTTAGTCCTTTT
1 ATTTTAAAATTAAACCCTTTT
9414 ATTTT
1 ATTTT
9419 TATTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTAAAATTAAACCCTTTT
Found at i:9541 original size:18 final size:17
Alignment explanation
Indices: 9501--9548 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
9491 TTTTAAATTA
* *
9501 ATTTAATCATTTTTGTT
1 ATTTATTCATTTTTATT
*
9518 ATTTATTTATTTTTATT
1 ATTTATTCATTTTTATT
9535 ATATTATTCATTTT
1 AT-TTATTCATTTT
9549 AATATTAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (17 bp):
ATTTATTCATTTTTATT
Found at i:12634 original size:6 final size:6
Alignment explanation
Indices: 12613--12651 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
12603 GAACACCCAC
*
12613 CAAAAG CAACAAG CAAAAG CAAAAG CAAAAG CATAAG CA
1 CAAAAG CAA-AAG CAAAAG CAAAAG CAAAAG CAAAAG CA
12652 GGATACACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.62, C:0.21, G:0.15, T:0.03
Consensus pattern (6 bp):
CAAAAG
Found at i:17080 original size:21 final size:21
Alignment explanation
Indices: 17054--17105 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
17044 TGTGCCTAGA
17054 AGGCTTTGTGCCGGTGTTTTC
1 AGGCTTTGTGCCGGTGTTTTC
* * *
17075 AGGCTTTGTACTGGTGTTTTT
1 AGGCTTTGTGCCGGTGTTTTC
17096 AGGCTTTGTG
1 AGGCTTTGTG
17106 ACTAGTAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.08, C:0.13, G:0.33, T:0.46
Consensus pattern (21 bp):
AGGCTTTGTGCCGGTGTTTTC
Found at i:18633 original size:19 final size:19
Alignment explanation
Indices: 18609--18653 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
18599 CAAAGCCAAC
*
18609 TGTCACAACATCAGCTTAG
1 TGTCACAACATCAGCTCAG
*
18628 TGTCACGACATCAGCTCAG
1 TGTCACAACATCAGCTCAG
18647 TGTCACA
1 TGTCACA
18654 TTACCCAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (19 bp):
TGTCACAACATCAGCTCAG
Found at i:20744 original size:2 final size:2
Alignment explanation
Indices: 20739--20763 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20729 CTAGTGTGTG
20739 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20764 GCATATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21147 original size:22 final size:20
Alignment explanation
Indices: 21106--21161 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
21096 TTTAGTCATA
21106 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATATAAT
21126 TAATACAATTTATT-AT-T--T
1 TAATA-AA-TTATTAATATAAT
21144 TAATAAATTATTTAATAT
1 TAATAAATTA-TTAATAT
21162 TTCAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 8 0.26
19 1 0.03
20 6 0.19
21 4 0.13
22 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAATTATTAATATAAT
Found at i:21211 original size:16 final size:14
Alignment explanation
Indices: 21171--21211 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
21161 TTTCAATTTT
21171 ATTTT-AATAATAA
1 ATTTTAAATAATAA
21184 ATTTTAAA-AATAA
1 ATTTTAAATAATAA
21197 TATTTCTAAATAATA
1 -ATTT-TAAATAATA
21212 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.42
14 6 0.25
15 4 0.17
16 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:36327 original size:16 final size:15
Alignment explanation
Indices: 36306--36351 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
36296 GAAAAATTAT
36306 GTTTTCCATCCTTCTA
1 GTTTTCCATCCTTC-A
*
36322 GTTTTCTATCCCTTCA
1 GTTTTCCAT-CCTTCA
*
36338 ATTTTCCATCCTTC
1 GTTTTCCATCCTTC
36352 CAATCTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.13, C:0.33, G:0.04, T:0.50
Consensus pattern (15 bp):
GTTTTCCATCCTTCA
Found at i:51333 original size:64 final size:67
Alignment explanation
Indices: 51212--51339 Score: 190
Period size: 67 Copynumber: 1.9 Consensus size: 67
51202 AGCAGCATAC
51212 TACCCAAGACCCTCACTTGTTAGCCATTACAGTGGAAAAAACATTAATTTTTATATATTATTTTT
1 TACCCAAGACCCTCACTTGTTAGCCATTACAGTGGAAAAAACATT-ATTTTTATATATTATTTTT
51277 ACT
65 ACT
* * * *
51280 TACCTAAGACCCTCACTT-TTAGTCATTACAGTGGAAACAA-ATT-TTTTTTTATATTATTTT
1 TACCCAAGACCCTCACTTGTTAGCCATTACAGTGGAAAAAACATTATTTTTATATATTATTTT
51340 CATTTCCCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
64 16 0.29
66 3 0.05
67 20 0.36
68 17 0.30
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (67 bp):
TACCCAAGACCCTCACTTGTTAGCCATTACAGTGGAAAAAACATTATTTTTATATATTATTTTTA
CT
Found at i:51375 original size:25 final size:25
Alignment explanation
Indices: 51347--51397 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
51337 TTTCATTTCC
*
51347 CAATTAGATGAGAACATACATTTGT
1 CAATTAGATGAGAACAGACATTTGT
*
51372 CAATTAGTTGAGAACAGACATTTGT
1 CAATTAGATGAGAACAGACATTTGT
51397 C
1 C
51398 TATCATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (25 bp):
CAATTAGATGAGAACAGACATTTGT
Found at i:56337 original size:81 final size:81
Alignment explanation
Indices: 56197--56345 Score: 190
Period size: 81 Copynumber: 1.8 Consensus size: 81
56187 ATAAACCGAT
* * ** * ** * **
56197 AATCTTGGCACCTAGTGCCTAGTTGATAAACCGCGAATGTGAGCACAGCTCTGGTTGGTTTAACC
1 AATCCTGGCACCTAATGCCTAGCAGATAAACCGCAAAAATGAGCACAACTCTAATTGGTTTAACC
56262 AACGAATGATTCGTCA
66 AACGAATGATTCGTCA
* *
56278 AATCCTGGCACCTAATGCCTAGCAGATATACCGCAAAAATGAGCCCAACTCTAATTGGTTTAACC
1 AATCCTGGCACCTAATGCCTAGCAGATAAACCGCAAAAATGAGCACAACTCTAATTGGTTTAACC
56343 AAC
66 AAC
56346 AATCATTGTA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 56 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (81 bp):
AATCCTGGCACCTAATGCCTAGCAGATAAACCGCAAAAATGAGCACAACTCTAATTGGTTTAACC
AACGAATGATTCGTCA
Found at i:64636 original size:29 final size:32
Alignment explanation
Indices: 64566--64649 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 32
64556 ATTTATCAAC
*
64566 CCCACTCATATATATTATATATAACACCAAAA
1 CCCACACATATATATTATATATAACACCAAAA
** *
64598 CCCATGCATATATATTATATA-AA-A-TAAAA
1 CCCACACATATATATTATATATAACACCAAAA
* *
64627 CTCACACATATATATTATCTATA
1 CCCACACATATATATTATATATA
64650 TAATAAAGTC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 21 0.48
30 2 0.05
31 2 0.05
32 19 0.43
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.32
Consensus pattern (32 bp):
CCCACACATATATATTATATATAACACCAAAA
Found at i:79987 original size:29 final size:29
Alignment explanation
Indices: 79931--79987 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
79921 AAATTGTATT
* * *
79931 AGTTTTGTAGTTTTTTTTTTTTCTAAAAA
1 AGTTTTGTAGTTTTTTATTATTCAAAAAA
*
79960 AGTTTTGTAGTTTTTTATTATTGAAAAA
1 AGTTTTGTAGTTTTTTATTATTCAAAAA
79988 GTATTACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (29 bp):
AGTTTTGTAGTTTTTTATTATTCAAAAAA
Found at i:80574 original size:2 final size:2
Alignment explanation
Indices: 80569--80602 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
80559 TGTAAAAAAG
80569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80603 CCGTTAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80820 original size:24 final size:24
Alignment explanation
Indices: 80775--80821 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
80765 TCTAAATTTT
*
80775 TAATATTTTAAAATAATAATAATA
1 TAATATTTTAAAACAATAATAATA
*
80799 TAATACTTTTAAGACAAT-ATAAT
1 TAATA-TTTTAAAACAATAATAAT
80822 TTTAATCTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TAATATTTTAAAACAATAATAATA
Done.