Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011395.1 Kokia drynarioides strain JFW-HI SEQ_126377, 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: 36193
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:4034 original size:2 final size:2
Alignment explanation
Indices: 4027--4059 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4017 TACATCAAAT
4027 TA TA TA TA 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 TA TA TA TA T
4060 TACAAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7438 original size:97 final size:96
Alignment explanation
Indices: 7272--7561 Score: 456
Period size: 97 Copynumber: 3.0 Consensus size: 96
7262 TTTTTTGGTG
* *
7272 AATTATAAGGGGAGAGCAAAGTTCTAACAGCAACACGATTGACGTAACTCGAA-CTCAGATCACA
1 AATTATAAGGGGAGAGCAAAGCTCTAACAGCAGCACGATTGACGTAACTCGAACCT-AGATCACA
7336 TCTGGGGTAATGAACATCCTTAACTATCAGATT
65 TCTGGGGTAATGAACA-CCTTAACTATCAGATT
* *
7369 AATTATAAGGGGAGAACAAAGCTCTAACAGCAGCACGATTGACGTAACTCGAACCTAAATCACAT
1 AATTATAAGGGGAGAGCAAAGCTCTAACAGCAGCACGATTGACGTAACTCGAACCTAGATCACAT
* *
7434 CTGGGGTAACGAACACCCTTAACTATCATATT
66 CTGGGGTAATGAACA-CCTTAACTATCAGATT
* *
7466 AATTATAAGGGGAGAGCAAAGCTCTAACAGCAGCACGATTGACGCAATTCGAACCTAGATCACAT
1 AATTATAAGGGGAGAGCAAAGCTCTAACAGCAGCACGATTGACGTAACTCGAACCTAGATCACAT
*
7531 CTAGGGTAATGAACACTCTTAACTATCAGAT
66 CTGGGGTAATGAACAC-CTTAACTATCAGAT
7562 CAACACACGA
Statistics
Matches: 177, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
96 1 0.01
97 174 0.98
98 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (96 bp):
AATTATAAGGGGAGAGCAAAGCTCTAACAGCAGCACGATTGACGTAACTCGAACCTAGATCACAT
CTGGGGTAATGAACACCTTAACTATCAGATT
Found at i:12073 original size:84 final size:83
Alignment explanation
Indices: 11981--12237 Score: 286
Period size: 84 Copynumber: 3.1 Consensus size: 83
11971 TAGAACTTAA
* **
11981 TTAATTCTTGTTTGGAAACAAAATCAAAATCA-AATCAAATCTGTTGAATGGTGGGAATAAATCC
1 TTAATTCTTGTTTGGAAACAAAATCAAAAT-AGAATAAAATCTGTTGAATGGCAGGAATAAATCC
*
12045 GGAAACAGAATTATTTAATT
65 -GAAACAGAATTATTCAATT
** * * * * *
12065 TTAATTCTTGTTCAGAAACTAAATCAAAATAGAATAAAATCTGTTTAACGGCAGAAAAAAATCCC
1 TTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTGTTGAATGGCAGGAATAAAT-CC
* *
12130 GAAACA-AATTTATCCAA-C
65 GAAACAGAA-TTATTCAATT
* *
12148 TTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAAATATGTTGAATGGCCGGAATAAATCTC
1 TTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTGTTGAATGGCAGGAATAAATC-C
* * *
12213 GATACTGATTTATTCAATT
65 GAAACAGAATTATTCAATT
12232 TTAATT
1 TTAATT
12238 TTTTATTCTC
Statistics
Matches: 140, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
82 1 0.01
83 68 0.49
84 69 0.49
85 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (83 bp):
TTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTGTTGAATGGCAGGAATAAATCCG
AAACAGAATTATTCAATT
Found at i:12930 original size:32 final size:32
Alignment explanation
Indices: 12889--12949 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
12879 AGGAGCCTTT
12889 AAATCAATTTGAATAGAATCAAATCAAATCGA
1 AAATCAATTTGAATAGAATCAAATCAAATCGA
* *
12921 AAATCAATTTGATTGGAATCAAATCAAAT
1 AAATCAATTTGAATAGAATCAAATCAAAT
12950 TAAGATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (32 bp):
AAATCAATTTGAATAGAATCAAATCAAATCGA
Found at i:15328 original size:20 final size:20
Alignment explanation
Indices: 15303--15346 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
15293 AACTTGACCT
15303 AAATTACAATT-TTAATAATA
1 AAATTA-AATTGTTAATAATA
*
15323 AAATTAATTTGTTAATAATA
1 AAATTAAATTGTTAATAATA
15343 AAAT
1 AAAT
15347 ATATTAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATTAAATTGTTAATAATA
Found at i:19712 original size:5 final size:5
Alignment explanation
Indices: 19704--19759 Score: 67
Period size: 5 Copynumber: 11.2 Consensus size: 5
19694 GGAGTAGGAC
* * * * *
19704 ATGAT ATGAT ATGAT ATGAT GTGAT TTGAT ATGGT ATGAT ACGTT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
19754 ATGAT A
1 ATGAT A
19760 ATATATGACC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (5 bp):
ATGAT
Found at i:21517 original size:18 final size:18
Alignment explanation
Indices: 21475--21517 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
21465 CCATAGTGGT
* *
21475 AGACAAAAACGTGCCATA
1 AGACAGAAACGTGCCAAA
21493 AGACAGAAACGTGCCACAA
1 AGACAGAAACGTGCCA-AA
21512 AG-CAGA
1 AGACAGA
21518 GGAAAAGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.49, C:0.23, G:0.21, T:0.07
Consensus pattern (18 bp):
AGACAGAAACGTGCCAAA
Found at i:22358 original size:16 final size:18
Alignment explanation
Indices: 22317--22359 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
22307 TTACTTTTTA
*
22317 ATATT-TTTTAAATTTCT
1 ATATTATTTAAAATTTCT
22334 ATATTATTTAAAATTTCT
1 ATATTATTTAAAATTTCT
22352 -T-TTATTTA
1 ATATTATTTA
22360 TAAAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 6 0.25
18 11 0.46
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTATTTAAAATTTCT
Found at i:22390 original size:16 final size:17
Alignment explanation
Indices: 22322--22397 Score: 68
Period size: 16 Copynumber: 4.5 Consensus size: 17
22312 TTTTAATATT
22322 TTTTAAATTTCTATATTA
1 TTTTAAATTTCTAT-TTA
*
22340 TTTAAAATTTCT-TTTA
1 TTTTAAATTTCTATTTA
*
22356 TTTATAAAATAT-TATTTA
1 TTT-T-AAATTTCTATTTA
*
22374 TTTTAAATTT-TACTTA
1 TTTTAAATTTCTATTTA
*
22390 TGTTAAAT
1 TTTTAAAT
22398 ATGTTTTATA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
16 23 0.47
17 3 0.06
18 23 0.47
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTCTATTTA
Found at i:23919 original size:29 final size:29
Alignment explanation
Indices: 23857--24260 Score: 201
Period size: 30 Copynumber: 13.7 Consensus size: 29
23847 TACTTGGGGC
*
23857 AAAATGGTAATTTTGGGAAAGTTCGA-GGTCA
1 AAAATGG-AATTTTTGGAAA-TTCGAGGGT-A
* *
23888 AAAATGGAATTTTTAGACATTCGAGGGT-
1 AAAATGGAATTTTTGGAAATTCGAGGGTA
* *
23916 AAAATGGTAATTTTTGGAAAGTTCG-GAGTTT
1 AAAATGG-AATTTTTGGAAA-TTCGAG-GGTA
* * * *
23947 AAAATAGAATTTTTAGACATTCGGGGGT-
1 AAAATGGAATTTTTGGAAATTCGAGGGTA
*
23975 -AAATGGTAATTTTTGGAAAAATCG-GGGTAA
1 AAAATGG-AATTTTTGG-AAATTCGAGGGT-A
* *
24005 AAAATGGAATTTTTGGAAGTTCGGGGGT-
1 AAAATGGAATTTTTGGAAATTCGAGGGTA
**
24033 AAAATGGGAATTTTTGGAAAAACCGA-GGTCA
1 AAAAT-GGAATTTTTGG-AAATTCGAGGGT-A
*** **
24064 AAAATGGAATTTTCAAAAATTTAAGGGT-
1 AAAATGGAATTTTTGGAAATTCGAGGGTA
*
24092 AAAATGGTAATTTTTTGGAAAAATCGA-GGTCA
1 AAAATGG-AA-TTTTTGG-AAATTCGAGGGT-A
*
24124 AAAATGGAA-TTTTGGAAAGTTAGAGGGTA
1 AAAATGGAATTTTTGGAAA-TTCGAGGGTA
* * * * *
24153 AAAATGTAAGTTTTAGAAAATT-TAGGTTTA
1 AAAATGGAA-TTTTTGGAAATTCGAGG-GTA
* * *
24183 AAAATGGAA-TTTTAGAAAGTT-TAGGGGTT
1 AAAATGGAATTTTTGGAAA-TTCGA-GGGTA
* *
24212 AAAATGTAATTTTTGGAAAAATT-TAGGGTTA
1 AAAATGGAATTTTTGG--AAATTCGAGGG-TA
24243 AAAATGG-ATTTTTGGAAA
1 AAAATGGAATTTTTGGAAA
24261 GTTTGGGGTC
Statistics
Matches: 290, Mismatches: 50, Indels: 69
0.71 0.12 0.17
Matches are distributed among these distances:
27 5 0.02
28 43 0.15
29 86 0.30
30 97 0.33
31 49 0.17
32 10 0.03
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAATTCGAGGGTA
Found at i:23935 original size:59 final size:60
Alignment explanation
Indices: 23857--24263 Score: 363
Period size: 59 Copynumber: 6.9 Consensus size: 60
23847 TACTTGGGGC
* ** *
23857 AAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGGAATTTTTAGACA-TTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAAGTTCGAGGGT
** ** * * *
23916 AAAATGGTAATTTTTGGAAAGTTCG-GAGTTTAAAATAGAATTTTTAGACA-TTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAG-GTCAAAAATGGAATTTTTAGAAAGTTCGAGGGT
* * * *
23975 -AAATGGTAATTTTTGGAAAAATCGGGGTAAAAAATGGAATTTTT-GGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAAGTTCGAGGGT
* * * * **
24033 AAAATGGGAATTTTTGGAAAAACCGAGGTCAAAAATGGAATTTTCA-AAAATTTAAGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAAGTTCGAGGGT
* *
24092 AAAATGGTAATTTTTTGGAAAAATCGAGGTCAAAAATGGAA-TTTTGGAAAGTTAGAGGGT
1 AAAATGGTAA-TTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAAGTTCGAGGGT
* * ** * *
24152 AAAAAT-GTAAGTTTTAG-AAAATTTAGGTTTAAAAATGGAA-TTTTAGAAAGTT-TAGGGGTT
1 -AAAATGGTAATTTTTGGAAAAATCGAGG-TCAAAAATGGAATTTTTAGAAAGTTCGA-GGG-T
** * *
24212 AAAAT-GTAATTTTTGGAAAAATTTAGGGTTAAAAATGG-ATTTTTGGAAAGTT
1 AAAATGGTAATTTTTGGAAAAATCGA-GGTCAAAAATGGAATTTTTAGAAAGTT
24264 TGGGGTCAAA
Statistics
Matches: 295, Mismatches: 39, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
57 2 0.01
58 56 0.19
59 157 0.53
60 73 0.25
61 7 0.02
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.33
Consensus pattern (60 bp):
AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTAGAAAGTTCGAGGGT
Found at i:24187 original size:30 final size:29
Alignment explanation
Indices: 24123--24297 Score: 122
Period size: 29 Copynumber: 5.9 Consensus size: 29
24113 AATCGAGGTC
* * * *
24123 AAAAATGGAATTTT-GGAAAGTTAGAGGGT
1 AAAAATGTAATTTTAGAAAATTTAG-GGTT
*
24152 AAAAATGTAAGTTTTAGAAAATTTAGGTTT
1 AAAAATGTAA-TTTTAGAAAATTTAGGGTT
* *
24182 AAAAATGGAATTTTAGAAAGTTTAGGGGTT
1 AAAAATGTAATTTTAGAAAATTTA-GGGTT
*
24212 -AAAATGTAATTTTTGGAAAAATTTAGGGTT
1 AAAAATGTAA-TTTTAG-AAAATTTAGGGTT
* * * * * *
24242 AAAAATGGATTTTTGGAAAGTTTGGGGTC
1 AAAAATGTAATTTTAGAAAATTTAGGGTT
* * *
24271 AAAATATG-ATTTTTGGACAATTTAGGG
1 AAAA-ATGTAATTTTAGAAAATTTAGGG
24298 ACCTCCAGGG
Statistics
Matches: 120, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
29 60 0.50
30 38 0.32
31 22 0.18
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAAATGTAATTTTAGAAAATTTAGGGTT
Found at i:24269 original size:59 final size:60
Alignment explanation
Indices: 23826--24297 Score: 282
Period size: 59 Copynumber: 8.0 Consensus size: 60
23816 AATAATCGGA
* * * * * * *
23826 GTCAAAAATGAGATTTTTGGATA-CTTGGGG-CAAAATGGTAA-TTTTGG-GAAAGTTCGAG
1 GTCAAAAATG-GAATTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGAAAAATTTAG-G
* * * * *
23884 GTCAAAAATGGAATTTTTAGACA-TTCGAGGG-TAAAATGGTAATTTTTGG--AAAGTTCGG
1 GTCAAAAATGGAA-TTTTGGAAAGTTTG-GGGTTAAAATGGTAATTTTTGGAAAAATTTAGG
** * * * * * **
23942 AGTTTAAAATAGAATTTTTAGACA-TTCGGGGGT-AAATGGTAATTTTTGGAAAAA-TCGGG
1 -GTCAAAAATGGAA-TTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGAAAAATTTAGG
* * * * ***
24001 GTAAAAAATGGAATTTTTGG-AAGTTCGGGGGTAAAATGGGAATTTTTGGAAAAACCGA-G
1 GTCAAAAATGGAA-TTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGAAAAATTTAGG
** * * **
24060 GTCAAAAATGGAATTTTCAAAAATTTAAGGG-TAAAATGGTAATTTTTTGGAAAAATCGA-G
1 GTCAAAAATGGAATTTTGGAAAGTTT-GGGGTTAAAATGGTAA-TTTTTGGAAAAATTTAGG
* * * *
24120 GTCAAAAATGGAATTTTGGAAAGTTAGAGGGTAAAAAT-GTAAGTTTTAG-AAAATTTAGG
1 GTCAAAAATGGAATTTTGGAAAGTTTG-GGGTTAAAATGGTAATTTTTGGAAAAATTTAGG
* * *
24179 TTTAAAAATGGAATTTTAGAAAGTTTAGGGGTTAAAAT-GTAATTTTTGGAAAAATTTAGG
1 GTCAAAAATGGAATTTTGGAAAGTTT-GGGGTTAAAATGGTAATTTTTGGAAAAATTTAGG
* * * * * *
24239 GTTAAAAATGGATTTTTGGAAAGTTTGGGGTCAAAAT-ATGATTTTTGG-ACAATTTAGG
1 GTCAAAAATGGAATTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGAAAAATTTAGG
24297 G
1 G
24298 ACCTCCAGGG
Statistics
Matches: 344, Mismatches: 52, Indels: 36
0.80 0.12 0.08
Matches are distributed among these distances:
57 3 0.01
58 84 0.24
59 161 0.47
60 91 0.26
61 5 0.01
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (60 bp):
GTCAAAAATGGAATTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGAAAAATTTAGG
Found at i:25879 original size:23 final size:24
Alignment explanation
Indices: 25852--25905 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
25842 GCAAGTTGCT
25852 GGTGGTGGCACTTCTG-GT-GCTGA
1 GGTGGTGGCAC-TCTGAGTGGCTGA
* *
25875 TGTGG-CGCACTCTGAGTGGCTGA
1 GGTGGTGGCACTCTGAGTGGCTGA
25898 GGTGGTGG
1 GGTGGTGG
25906 TAGTGACACA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
21 4 0.17
22 6 0.25
23 13 0.54
24 1 0.04
ACGTcount: A:0.09, C:0.17, G:0.46, T:0.28
Consensus pattern (24 bp):
GGTGGTGGCACTCTGAGTGGCTGA
Found at i:26112 original size:18 final size:18
Alignment explanation
Indices: 26089--26170 Score: 87
Period size: 18 Copynumber: 4.5 Consensus size: 18
26079 ATTAAATTTT
26089 AATTTAAAATAAATTTAA
1 AATTTAAAATAAATTTAA
26107 AATTTAAAATAAATTTAA
1 AATTTAAAATAAATTTAA
* * *
26125 ACTTACTCAAATTAAGTTT-A
1 AATT--T-AAAATAAATTTAA
26145 AATTTAAAATAAA-TTAA
1 AATTTAAAATAAATTTAA
*
26162 AGTTTAAAA
1 AATTTAAAA
26171 ACAATCCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.04
17 15 0.28
18 22 0.42
20 5 0.09
21 9 0.17
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (18 bp):
AATTTAAAATAAATTTAA
Found at i:26862 original size:98 final size:98
Alignment explanation
Indices: 26692--27215 Score: 666
Period size: 98 Copynumber: 5.4 Consensus size: 98
26682 AATTTTCGCT
* * * *
26692 GTACT-GGATTCGCCGTTGCGGCTTAAATCTTTCCC-TT-TGTCTTTGTGGTACTGGATTCGCCG
1 GTACTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
* **
26754 TTGCGGCTTAAATATTTCTATTCATG-TCTCTGAG
65 TTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAG
*
26788 GTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTATTGGATTCGCCGT
1 GTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGT
* *
26853 TGCGGCTTAAATCTTTCCCTTCGTG-TCTCTGAT
66 TGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAG
*
26886 GTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCAT
1 GTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGT
26951 TGCGGCTTAAATC-TTCCCTTCATGCTTCTGAG
66 TGCGGCTTAAATCTTTCCCTTCATGCTTCTGAG
* * * *** * * *
26983 GTACAAGGTTCGCCGTTGCGACTTAAACTTTTCCCTCCATATCTTTGTGGTACTGGATTCGTCGT
1 GTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGT
* *
27048 TGCAGCTTAAATCTTTCCCTTCATGCTTCTGTG
66 TGCGGCTTAAATCTTTCCCTTCATGCTTCTGAG
** * * * * *
27081 GTA-TAAGGTTCGCCATTATGACTTAAACATTTCCCTTCGTATCTTCGCGGTACTGGATTCACCG
1 GTACT-AGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
27145 TTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAG
65 TTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAG
* * *
27179 GTACAAGGTTTGCCATTGCGACTTAAACTTTTTCCCT
1 GTACTAGGTTCGCCATTGCGACTTAAAC-CTTTCCCT
27216 CCGTGTTTTG
Statistics
Matches: 376, Mismatches: 44, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
96 29 0.08
97 86 0.23
98 254 0.68
99 7 0.02
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (98 bp):
GTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGT
TGCGGCTTAAATCTTTCCCTTCATGCTTCTGAG
Found at i:27004 original size:195 final size:194
Alignment explanation
Indices: 26691--27217 Score: 679
Period size: 195 Copynumber: 2.7 Consensus size: 194
26681 CAATTTTCGC
* * * *
26691 TGTACT-GGATTCGCCGTTGCGGCTTAAATCTTTCCC-TT-TGTCTTTGTGGTACTGGATTCGCC
1 TGTACTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCC
* ** * *
26753 GTTGCGGCTTAAATATTTCTATTCATG-TCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACC
65 GTTGCGGCTTAAAT-CTTCCCTTCATGCT-TCTGAGGTACAAGGTTCGCCATTGCGACTTAAACT
*** * * * *
26817 TTTCCCTTTGTGTCTTCGTGGTATTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCGTG-TCT
128 TTTCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGCT-T
26881 CTG
192 CTG
26884 ATGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCC
1 -TGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCC
* *
26949 ATTGCGGCTTAAATCTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACTTT
65 GTTGCGGCTTAAATCTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACTTT
* *
27014 TCCCTCCATATCTTTGTGGTACTGGATTCGTCGTTGCAGCTTAAATCTTTCCCTTCATGCTTCTG
130 TCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGCTTCTG
** * * * * *
27079 TGGTA-TAAGGTTCGCCATTATGACTTAAACATTTCCCTTCGTATCTTCGCGGTACTGGATTCAC
1 T-GTACT-AGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGC
*
27143 CGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTTGCCATTGCGACTTAAACT
64 CGTTGCGGCTTAAATC-TTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAAC-
27208 TTTTCCCTCC
127 TTTTCCCTCC
27218 GTGTTTTGTG
Statistics
Matches: 294, Mismatches: 30, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
194 32 0.11
195 169 0.57
196 83 0.28
197 10 0.03
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (194 bp):
TGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCG
TTGCGGCTTAAATCTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACTTTT
CCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGCTTCTG
Found at i:27182 original size:49 final size:49
Alignment explanation
Indices: 26692--27182 Score: 426
Period size: 49 Copynumber: 10.1 Consensus size: 49
26682 AATTTTCGCT
26692 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT--TGTCTT-TGTG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGTG
* ** *
26739 GTACTGGATTCGCCGTTGCGGCTTAAATATTTCTATTCATG-TCTCTGAG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGTG
* * * **
26788 GTACTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTC-GTG
1 GTACT-GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGTG
* *
26837 GTATTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCGTG-TCTCTGAT-
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTG-TG
* * * **
26886 GTACTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTC-GTG
1 GTACT-GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGTG
* *
26935 GTACTGGATTCGCCATTGCGGCTTAAATC-TTCCCTTCATGCTTCTGAG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGTG
* * * *
26983 GTACAAGG-TTCGCCGTTGCGACTTAAA-CTTTTCCCTCCATATCTT-TGTG
1 GTAC-TGGATTCGCCGTTGCGGCTTAAATC-TTTCCCTTCAT-GCTTCTGTG
* *
27032 GTACTGGATTCGTCGTTGCAGCTTAAATCTTTCCCTTCATGCTTCTGTG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGTG
* ** * *
27081 GTA-TAAGG-TTCGCCATTATGACTTAAA-CATTTCCCTTCGTAT-CTTC-GCG
1 GTACT--GGATTCGCCGTTGCGGCTTAAATC-TTTCCCTTC--ATGCTTCTGTG
* *
27130 GTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGTG
27179 GTAC
1 GTAC
27183 AAGGTTTGCC
Statistics
Matches: 357, Mismatches: 53, Indels: 66
0.75 0.11 0.14
Matches are distributed among these distances:
47 43 0.12
48 53 0.15
49 236 0.66
50 21 0.06
51 4 0.01
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (49 bp):
GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGTG
Found at i:27680 original size:18 final size:18
Alignment explanation
Indices: 27653--27689 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
27643 GAAAAATACC
*
27653 GAATATTTACAAGGAACA
1 GAATAATTACAAGGAACA
27671 GAATAATTACAAGGAACA
1 GAATAATTACAAGGAACA
27689 G
1 G
27690 TATTAGATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (18 bp):
GAATAATTACAAGGAACA
Found at i:34551 original size:30 final size:30
Alignment explanation
Indices: 34517--34576 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
34507 TGTACTGCTC
*
34517 CTCTATTTGTTTGGAAACTTCTAATTTTGT
1 CTCTATTTGTTTGGAAACTTCAAATTTTGT
34547 CTCTATTTGTTTGGAAACTTCAAATTTTGT
1 CTCTATTTGTTTGGAAACTTCAAATTTTGT
34577 TTTCTCTGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.52
Consensus pattern (30 bp):
CTCTATTTGTTTGGAAACTTCAAATTTTGT
Done.