Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008094.1 Kokia drynarioides strain JFW-HI SEQ_122752, 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: 75587
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:8794 original size:20 final size:21
Alignment explanation
Indices: 8769--8822 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
8759 GATTGATAAA
* *
8769 AAAGTCAACGGTTAAT-GGTC
1 AAAGTCAACGGTCAATGGGAC
*
8789 AAAGTCAATGGTCAATGGGAC
1 AAAGTCAACGGTCAATGGGAC
*
8810 AAAGTCAATGGTC
1 AAAGTCAACGGTC
8823 TAAGTCAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (21 bp):
AAAGTCAACGGTCAATGGGAC
Found at i:8800 original size:13 final size:13
Alignment explanation
Indices: 8799--8843 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
8789 AAAGTCAATG
*
8799 GTCAATGGGACAAA
1 GTCAAT-GGTCAAA
*
8813 GTCAATGGTCTAA
1 GTCAATGGTCAAA
8826 GTCAATGGTCAAA
1 GTCAATGGTCAAA
8839 GTCAA
1 GTCAA
8844 CTCGAGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (13 bp):
GTCAATGGTCAAA
Found at i:12805 original size:7 final size:7
Alignment explanation
Indices: 12793--12873 Score: 53
Period size: 7 Copynumber: 11.9 Consensus size: 7
12783 GGTAAAAAAA
12793 GTCAACG
1 GTCAACG
12800 GTCAACG
1 GTCAACG
*
12807 GTCAAAG
1 GTCAACG
*
12814 G-CAATG
1 GTCAACG
12820 GTCAACGG
1 GTCAAC-G
*
12828 GTCAA-A
1 GTCAACG
12834 GTCAACG
1 GTCAACG
* *
12841 ATCAATG
1 GTCAACG
*
12848 AGTCAA-A
1 -GTCAACG
*
12855 GTCAATG
1 GTCAACG
12862 GTCAA-G
1 GTCAACG
12868 GTCAAC
1 GTCAAC
12874 TAGGGTCAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
6 21 0.36
7 27 0.47
8 10 0.17
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:12832 original size:21 final size:21
Alignment explanation
Indices: 12790--12866 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
12780 ATTGGTAAAA
*
12790 AAAGTCAACGGTCAAC-GGTC
1 AAAGTCAATGGTCAACGGGTC
*
12810 AAAGGCAATGGTCAACGGGTC
1 AAAGTCAATGGTCAACGGGTC
* * * *
12831 AAAGTCAACGATCAATGAGTC
1 AAAGTCAATGGTCAACGGGTC
12852 AAAGTCAATGGTCAA
1 AAAGTCAATGGTCAA
12867 GGTCAACTAG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 14 0.30
21 33 0.70
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
AAAGTCAATGGTCAACGGGTC
Found at i:14372 original size:24 final size:24
Alignment explanation
Indices: 14343--14424 Score: 128
Period size: 24 Copynumber: 3.4 Consensus size: 24
14333 GACTAATAAA
* *
14343 AGTTTAACTAAAACAAATAAACAG
1 AGTTTAATTGAAACAAATAAACAG
*
14367 AGTTTAATTGAAACAAATAAACAA
1 AGTTTAATTGAAACAAATAAACAG
14391 AGTTTAATTGAAACAAATAAACAG
1 AGTTTAATTGAAACAAATAAACAG
*
14415 ACTTTAATTG
1 AGTTTAATTG
14425 GAAGATTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (24 bp):
AGTTTAATTGAAACAAATAAACAG
Found at i:17301 original size:13 final size:13
Alignment explanation
Indices: 17283--17307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17273 TACTCTTTAT
17283 GAAAGCAATTCAC
1 GAAAGCAATTCAC
17296 GAAAGCAATTCA
1 GAAAGCAATTCA
17308 TACAACTGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (13 bp):
GAAAGCAATTCAC
Found at i:19139 original size:195 final size:193
Alignment explanation
Indices: 18682--19196 Score: 580
Period size: 195 Copynumber: 2.7 Consensus size: 193
18672 TTCCAGGATT
* *
18682 CACTTATGCATAAGTCCCAGCCATCGTAGGGCCTGTAATCCATTCTATGATTCATATCTCTTTTT
1 CACTTAAGCATAAGTCCCAGCCATCGTAGGGCCTGTAATCCATTCTAGGATTCATATCTCTTTTT
* **
18747 TCGACT--C--ACTGCCCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGTCATCG
66 TCGACTCACATACTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAACCATCG
* * ** * * **
18808 GTACAATGTCTATCTATAAACTATCTCCTAATGATGCTGCTCACACGAGCTGTCGGGTGTATG
131 ATACAATATCTATCTATAAACTATCTCCTAACAATGCTGCTCACACAAGCTGTCGAGAATATG
* * *
18871 CACTTATGCATAAGTCCCAACCATCGTAGGACCTGTAATCCATTCTAGGATTCATATCTCTTTTT
1 CACTTAAGCATAAGTCCCAGCCATCGTAGGGCCTGTAATCCATTCTAGGATTCATATCTCTTTTT
*
18936 TCGACTCACAATACTGCTCACACGAGTTGTCGAGGACTCGTAACATATGCGGTACCTCAACCATC
66 TCGACTCAC-ATACTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAACCATC
** * * * * *
19001 GATACGGTATTTGTGC-ATATAATTGT-TCCCTAACAATGCTGCTCACATAAGCTGTCGAGAATA
130 GATACAATATCTAT-CTATA-AACTATCT-CCTAACAATGCTGCTCACACAAGCTGTCGAGAATA
19064 TG
192 TG
* * * * *
19066 CA-TTCAAGCATAAATCTCAGCCTTCGTAGGGCCTATAATCCATTTTTA-GATTTCATATCTCTT
1 CACTT-AAGCATAAGTCCCAGCCATCGTAGGGCCTGTAATCCA-TTCTAGGA-TTCATATCTCTT
* * * * * *
19129 TTCT-GACTCACGATACTACTCATACGAGCTGTCGAGGACTTGCAACATATGCAGTACCTCAACC
63 TTTTCGACTCAC-ATACTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAACC
19193 ATCG
127 ATCG
19197 CGTCGATTTC
Statistics
Matches: 277, Mismatches: 38, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
189 68 0.25
191 1 0.00
194 63 0.23
195 126 0.45
196 19 0.07
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (193 bp):
CACTTAAGCATAAGTCCCAGCCATCGTAGGGCCTGTAATCCATTCTAGGATTCATATCTCTTTTT
TCGACTCACATACTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAACCATCG
ATACAATATCTATCTATAAACTATCTCCTAACAATGCTGCTCACACAAGCTGTCGAGAATATG
Found at i:24446 original size:25 final size:25
Alignment explanation
Indices: 24368--24435 Score: 127
Period size: 25 Copynumber: 2.7 Consensus size: 25
24358 TCACGTTCAC
*
24368 ATTTTTTTTCTCAATGCTCCCCCAA
1 ATTTGTTTTCTCAATGCTCCCCCAA
24393 ATTTGTTTTCTCAATGCTCCCCCAA
1 ATTTGTTTTCTCAATGCTCCCCCAA
24418 ATTTGTTTTCTCAATGCT
1 ATTTGTTTTCTCAATGCT
24436 TTCACAGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.19, C:0.28, G:0.07, T:0.46
Consensus pattern (25 bp):
ATTTGTTTTCTCAATGCTCCCCCAA
Found at i:24620 original size:21 final size:21
Alignment explanation
Indices: 24594--24634 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
24584 TATTTGGTTA
24594 GTGAGAAAACTAAAGAAAATG
1 GTGAGAAAACTAAAGAAAATG
24615 GTGAGAAAACTAAAGAAAAT
1 GTGAGAAAACTAAAGAAAAT
24635 AGATTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.05, G:0.22, T:0.15
Consensus pattern (21 bp):
GTGAGAAAACTAAAGAAAATG
Found at i:27231 original size:422 final size:413
Alignment explanation
Indices: 26419--27249 Score: 1110
Period size: 422 Copynumber: 2.0 Consensus size: 413
26409 CATGTTCAGT
* * * *
26419 TAATAAAGGTTATAAAACATGAACTTATTTAACGATGGTTGACATGAAATGCCATTTGAAAATGA
1 TAATAAAGGTTATAAAACAAGAACTTACTTAACAATGATTGACATGAAATGCCATTTGAAAATGA
* ** *
26484 AATATTTTGCATGCATATGAAATGTGATAATTGACAACATATGAAAGATTTTGAACTAGTTAAAA
66 AATATTTTGCATGCATATGAAAAGTGATAATTGACAACATATGAAAGATGATGAAATAGTTAAAA
* * *
26549 ATGAGCCATGGGGGCTGATTTAAATATGAATAAGTCAGTAGTGTAACACCCTATACTTGACCTGA
131 ATGAGCCATGGGGGCTAATTTAAATATGAATAAGTCAGTAGTGTAACACCCAATACTTGACCCGA
* * * *
26614 TCGCTAGGTCCAAGCTATAGGATGCCATATTATTTGTCCGAGCAAGTATGAAAACAATTCCATTC
196 TCGCTAGGTCCAAGCTATAGGATGCCATATTATTTATCAGAGCAACTACGAAAACAATTCCATTC
* *
26679 ATTCATTAATTAAAACAAGTTTTAATTAATAAATCAATATAACATGTTATATTATCTTATTTAGG
261 ATTAATTAATTAAAACAAGTTTTAATTAATAAATCAATATAACATGTTATATTATCTTATCTAGG
* * *
26744 GCTTATACGAGCTAACAATAGCTCTTACGATAACCTGAGACCAATTGAGGACCTAACTGCAAAGT
326 GCTTATACGAACTAACAATAGCTCTTACGATAACATGAGACCAATTAAGGACCTAACTGCAAAGT
26809 TTTCAAAGTAAATCGTGTTCGGC
391 TTTCAAAGTAAATCGTGTTCGGC
* * * * * *
26832 TAATAAGGGTTATAAAATAAGAACTTGCTTAACAATGATTGATATGAAATGTCATTTGAACATGA
1 TAATAAAGGTTATAAAACAAGAACTTACTTAACAATGATTGACATGAAATGCCATTTGAAAATGA
*
26897 AATATTTTGCATGCATATGAAAAGTGATAATTGACAACATGTGAAAGATGATGCAAAATAGTTAA
66 AATATTTTGCATGCATATGAAAAGTGATAATTGACAACATATGAAAGATGATG--AAATAGTTAA
* * * *
26962 AAATGAGCCTTGGGGGC-AATTTCAATATGAATGAGTTAGTAGTGTAACACCCAATACTTGACCC
129 AAATGAGCCATGGGGGCTAATTTAAATATGAATAAGTCAGTAGTGTAACACCCAATACTTGACCC
* * * *
27026 GATTGTTGGGTCCAAGCTACTA-TATGCCATATT-TATTATCAGAGCAACTACGAAAACAATTTT
194 GATCGCTAGGTCCAAGCTA-TAGGATGCCATATTAT-TTATCAGAGCAACTACGAAAACAA---T
* * *
27089 AATTCATTCATTAATTAATTAAAACAAGTTTTAATAATTAATACATCATTATAACATGTTATATT
254 --TCCATTCATTAATTAATTAAAACAAG-TTT--TAATTAATAAATCAATATAACATGTTATATT
* ** * * * *
27154 ATCTTATCTAGGGCTTATATGAACTTTCTATAGCTCTTATGATAACATGAGACCATTTAAGTACC
314 ATCTTATCTAGGGCTTATACGAACTAACAATAGCTCTTACGATAACATGAGACCAATTAAGGACC
**
27219 TAACTGCAAAGTTTTCAAAGTAGTTCGTGTT
379 TAACTGCAAAGTTTTCAAAGTAAATCGTGTT
27250 GGCGACGCGA
Statistics
Matches: 359, Mismatches: 47, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
413 105 0.29
414 87 0.24
415 27 0.08
417 1 0.00
419 24 0.07
420 3 0.01
422 112 0.31
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (413 bp):
TAATAAAGGTTATAAAACAAGAACTTACTTAACAATGATTGACATGAAATGCCATTTGAAAATGA
AATATTTTGCATGCATATGAAAAGTGATAATTGACAACATATGAAAGATGATGAAATAGTTAAAA
ATGAGCCATGGGGGCTAATTTAAATATGAATAAGTCAGTAGTGTAACACCCAATACTTGACCCGA
TCGCTAGGTCCAAGCTATAGGATGCCATATTATTTATCAGAGCAACTACGAAAACAATTCCATTC
ATTAATTAATTAAAACAAGTTTTAATTAATAAATCAATATAACATGTTATATTATCTTATCTAGG
GCTTATACGAACTAACAATAGCTCTTACGATAACATGAGACCAATTAAGGACCTAACTGCAAAGT
TTTCAAAGTAAATCGTGTTCGGC
Found at i:27923 original size:15 final size:15
Alignment explanation
Indices: 27905--27936 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27895 AAGAGTTTGC
27905 ATTAACATATGGTGT
1 ATTAACATATGGTGT
*
27920 ATTAACATTTGGTGT
1 ATTAACATATGGTGT
27935 AT
1 AT
27937 GCATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (15 bp):
ATTAACATATGGTGT
Found at i:45833 original size:5 final size:5
Alignment explanation
Indices: 45823--45850 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
45813 ATTAAAGATT
45823 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
45851 TATTTAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:48219 original size:57 final size:56
Alignment explanation
Indices: 48120--48286 Score: 160
Period size: 57 Copynumber: 2.9 Consensus size: 56
48110 ATATTCTAAC
* * * * * * *
48120 ATCAATCCATAAGATTAAACCAATTGCA-ATTAACTCGTTTCAATAGCATATCCCA-TT
1 ATCAATCGATAAGGTTATACCAATTACACA-TAATTCATTTCAAT-GCATAT-CAAGTT
* *
48177 ATCAATCTA-AATGGTTATACCATTTACACATAATTCATTTCAATGACATATCAAGTT
1 ATCAATCGATAA-GGTTATACCAATTACACATAATTCATTTCAATG-CATATCAAGTT
* * *
48234 ATCAATCGATAAGGTTATACTAATTACATATAATTCATTTCAATGCATGTCAA
1 ATCAATCGATAAGGTTATACCAATTACACATAATTCATTTCAATGCATATCAA
48287 ATTAGTTTAC
Statistics
Matches: 92, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
56 12 0.13
57 77 0.84
58 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.35
Consensus pattern (56 bp):
ATCAATCGATAAGGTTATACCAATTACACATAATTCATTTCAATGCATATCAAGTT
Found at i:50207 original size:16 final size:17
Alignment explanation
Indices: 50180--50214 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
50170 CTTGAAATTT
50180 TAAAAAATTATAAAATA
1 TAAAAAATTATAAAATA
50197 TAAAAAA-TATAAAATA
1 TAAAAAATTATAAAATA
50213 TA
1 TA
50215 TTTTAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATTATAAAATA
Found at i:50900 original size:22 final size:21
Alignment explanation
Indices: 50875--50919 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
50865 ACAAATAAAA
*
50875 AATATAAAATTATTAAATGTTT
1 AATATAAAAATATTAAAT-TTT
*
50897 AATATAAAAATATTATATTTT
1 AATATAAAAATATTAAATTTT
50918 AA
1 AA
50920 AAAAATATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATAAAAATATTAAATTTT
Found at i:57911 original size:29 final size:30
Alignment explanation
Indices: 57878--57963 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 30
57868 ATTTAATGTG
57878 CAATTGTATACGT-AAACTTTAATTTGGTAT
1 CAATTGTATACGTCAAACTTTAATTTGGT-T
* * *
57908 -AATTATATACGTGAAACTCTAATTATGGTT
1 CAATTGTATACGTCAAACTTTAATT-TGGTT
* * *
57938 CAAATGTATTCTTCAAACTTTAATTT
1 CAATTGTATACGTCAAACTTTAATTT
57964 TACTTTAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 11 0.24
30 12 0.27
31 22 0.49
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (30 bp):
CAATTGTATACGTCAAACTTTAATTTGGTT
Found at i:57931 original size:30 final size:30
Alignment explanation
Indices: 57879--57936 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
57869 TTTAATGTGC
* *
57879 AATTGTATACGTAAACTTTAATT-TGGTAT
1 AATTATATACGTAAACTCTAATTATGGTAT
57908 AATTATATACGTGAAACTCTAATTATGGT
1 AATTATATACGT-AAACTCTAATTATGGT
57937 TCAAATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 10 0.40
31 4 0.16
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (30 bp):
AATTATATACGTAAACTCTAATTATGGTAT
Found at i:62727 original size:11 final size:12
Alignment explanation
Indices: 62667--62727 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 12
62657 ATTCCAAAAA
62667 TAATA-TTATTT
1 TAATATTTATTT
*
62678 TAATAATTTAATAT
1 TAAT-ATTT-ATTT
62692 TAA-ATTTATTT
1 TAATATTTATTT
* *
62703 TAATACTGATTT
1 TAATATTTATTT
62715 TAATA-TTATTT
1 TAATATTTATTT
62726 TA
1 TA
62728 TTAATTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 17 0.41
12 16 0.39
13 2 0.05
14 6 0.15
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (12 bp):
TAATATTTATTT
Found at i:62750 original size:20 final size:18
Alignment explanation
Indices: 62668--62777 Score: 66
Period size: 19 Copynumber: 5.9 Consensus size: 18
62658 TTCCAAAAAT
* *
62668 AATATTATTTTAATAATTT
1 AATATTAATTTAAT-ATTA
*
62687 AATATTAAATTT-AT-TTT
1 AATATT-AATTTAATATTA
* *
62704 AATACTGATTTTAATATTA
1 AATA-TTAATTTAATATTA
**
62723 TTTTATTAATTTAATATTA
1 -AATATTAATTTAATATTA
62742 AAGTGATT-ATCTTAATATTA
1 AA-T-ATTAAT-TTAATATTA
62762 AAT-TTAATTTAATATT
1 AATATTAATTTAATATT
62778 TATCTTGTAG
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
17 21 0.29
18 5 0.07
19 26 0.36
20 20 0.28
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (18 bp):
AATATTAATTTAATATTA
Found at i:62768 original size:51 final size:48
Alignment explanation
Indices: 62667--62769 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 48
62657 ATTCCAAAAA
* * *
62667 TAATATTATTTTAATAATTTAATATTAAATTTATTTTAATACTGATTT
1 TAATATTATTTTAATAATTTAATATTAAATTTATCTTAATACTAAATT
* *
62715 TAATATTATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATT
1 TAATATTATTTTAATAATTTAATATTAAA-T--TTATCTTAATACTAAATT
62766 TAAT
1 TAAT
62770 TTAATATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
48 28 0.60
49 1 0.02
51 18 0.38
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (48 bp):
TAATATTATTTTAATAATTTAATATTAAATTTATCTTAATACTAAATT
Found at i:69792 original size:24 final size:24
Alignment explanation
Indices: 69760--69902 Score: 142
Period size: 24 Copynumber: 6.0 Consensus size: 24
69750 ATTTCATTAC
* *
69760 GTTTACGCTCATCAGGTTATATAT
1 GTTTACGCTCGTCAGCTTATATAT
*
69784 GTTTACGCTCGTCAGCTTATATAC
1 GTTTACGCTCGTCAGCTTATATAT
* * * * ** *
69808 GTTTATGTTCATTAGCTTGCACAT
1 GTTTACGCTCGTCAGCTTATATAT
*
69832 GTTTACACTCGTCAGCTTATATAT
1 GTTTACGCTCGTCAGCTTATATAT
** * *
69856 GTTTACGCTCGTCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTATATAT
*
69880 ATTTACGCTCGTCAGCTTATATA
1 GTTTACGCTCGTCAGCTTATATA
69903 CAATTACGCT
Statistics
Matches: 91, Mismatches: 28, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 91 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (24 bp):
GTTTACGCTCGTCAGCTTATATAT
Found at i:69835 original size:48 final size:48
Alignment explanation
Indices: 69757--69912 Score: 186
Period size: 48 Copynumber: 3.2 Consensus size: 48
69747 ACAATTTCAT
* ** *
69757 TACGTTTACGCTCATCAGGTTATATATGTTTACGCTCGTCAGCTTATA
1 TACGTTTACGCTCATCAGCTTGCACATGTTTACGCTCGTCAGCTTATA
* * * *
69805 TACGTTTATGTTCATTAGCTTGCACATGTTTACACTCGTCAGCTTATA
1 TACGTTTACGCTCATCAGCTTGCACATGTTTACGCTCGTCAGCTTATA
* * **
69853 TATGTTTACGCTCGTCAGCTTGCACACATTTACGCTCGTCAGCTTATA
1 TACGTTTACGCTCATCAGCTTGCACATGTTTACGCTCGTCAGCTTATA
**
69901 TACAATTACGCT
1 TACGTTTACGCT
69913 ATTATGAAAT
Statistics
Matches: 89, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 89 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (48 bp):
TACGTTTACGCTCATCAGCTTGCACATGTTTACGCTCGTCAGCTTATA
Found at i:69897 original size:72 final size:72
Alignment explanation
Indices: 69760--69897 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 72
69750 ATTTCATTAC
* * * * * * * *
69760 GTTTACGCTCATCAGGTTATATATGTTTACGCTCGTCAGCTTATATACGTTTATGTTCATTAGCT
1 GTTTACACTCATCAGCTTATATATGTTTACGCTCGTCAGCTTACACACATTTACGCTCATCAGCT
69825 TGCACAT
66 TGCACAT
* * *
69832 GTTTACACTCGTCAGCTTATATATGTTTACGCTCGTCAGCTTGCACACATTTACGCTCGTCAGCT
1 GTTTACACTCATCAGCTTATATATGTTTACGCTCGTCAGCTTACACACATTTACGCTCATCAGCT
69897 T
66 T
69898 ATATACAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (72 bp):
GTTTACACTCATCAGCTTATATATGTTTACGCTCGTCAGCTTACACACATTTACGCTCATCAGCT
TGCACAT
Done.