Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005718.1 Kokia drynarioides strain JFW-HI SEQ_119948, 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: 46330
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:603 original size:22 final size:20
Alignment explanation
Indices: 576--615 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
566 GCGAGTCTAA
576 AATAATGTTAAATGTTTTTTTT
1 AATAATGTT-AAT-TTTTTTTT
598 AATAATGTTAATTTTTTT
1 AATAATGTTAATTTTTTT
616 AATTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
AATAATGTTAATTTTTTTTT
Found at i:614 original size:18 final size:17
Alignment explanation
Indices: 591--627 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
581 TGTTAAATGT
591 TTTTTTTAATAATGTTAA
1 TTTTTTTAATAAT-TTAA
*
609 TTTTTTTAATTATTTAA
1 TTTTTTTAATAATTTAA
626 TT
1 TT
628 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTTTTAATAATTTAA
Found at i:14414 original size:22 final size:21
Alignment explanation
Indices: 14384--14424 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
14374 TTTTGAAAAA
* *
14384 ATAAAATAAATTTATATTTAT
1 ATAAAATAAAATAATATTTAT
14405 ATAATAATAAAATAATATTT
1 ATAA-AATAAAATAATATTT
14425 TAACGGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAATAAAATAATATTTAT
Found at i:14747 original size:29 final size:30
Alignment explanation
Indices: 14688--14757 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
14678 ATTTTCCTCC
* * *
14688 TAGTTTTTATGGCTAAGCTAGATCCGTTTT
1 TAGTTTTTATTGCTAAGCTAAAACCGTTTT
14718 TAGTTTTTATTGCTCAA-CTAAAACC-TTTT
1 TAGTTTTTATTGCT-AAGCTAAAACCGTTTT
* *
14747 TAATTTATATT
1 TAGTTTTTATT
14758 TGGTGATAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 13 0.38
30 19 0.56
31 2 0.06
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (30 bp):
TAGTTTTTATTGCTAAGCTAAAACCGTTTT
Found at i:19614 original size:18 final size:19
Alignment explanation
Indices: 19575--19618 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
19565 ACATTAAAAA
19575 ATAAAAATGAAAATAAATAT
1 ATAAAAATGAAAAT-AATAT
*
19595 ATAAAAATTAAAAT-ATAT
1 ATAAAAATGAAAATAATAT
19613 ATAAAA
1 ATAAAA
19619 TCTAGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.43
20 13 0.57
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
ATAAAAATGAAAATAATAT
Found at i:19745 original size:22 final size:22
Alignment explanation
Indices: 19702--19771 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
19692 GAAATTAATA
*
19702 ATATTATT-AAAAAATAAAAAAT
1 ATATTTTTAAAAAAAT-AAAAAT
*
19724 GTATTTTTAAAAAAATAAAAAT
1 ATATTTTTAAAAAAATAAAAAT
* * *
19746 ATTTTTTTATAAAATTAAAAAT
1 ATATTTTTAAAAAAATAAAAAT
19768 ATAT
1 ATAT
19772 AATAATACAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 33 0.82
23 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (22 bp):
ATATTTTTAAAAAAATAAAAAT
Found at i:20279 original size:23 final size:21
Alignment explanation
Indices: 20232--20287 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
20222 ATATATAAAC
*
20232 AAATGTTTAAAATATTTTTTAT
1 AAAT-TTTAAAATATTATTTAT
20254 AAAATTTTAAAATATATAATTT-T
1 -AAATTTTAAAATAT-T-ATTTAT
20277 AAATTTTAAAA
1 AAATTTTAAAA
20288 ATCCAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 21 0.70
23 6 0.20
24 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATTTTAAAATATTATTTAT
Found at i:20459 original size:26 final size:25
Alignment explanation
Indices: 20413--20462 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
20403 ATTATGTATT
*
20413 TTACAATTTTATTTTATTTTTTAAA
1 TTACAATTTTATTATATTTTTTAAA
20438 TTACAATTTT-TATATATCTTTTTAA
1 TTACAATTTTAT-TATAT-TTTTTAA
20463 TAATACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 14 0.64
26 7 0.32
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (25 bp):
TTACAATTTTATTATATTTTTTAAA
Found at i:23811 original size:21 final size:21
Alignment explanation
Indices: 23761--23827 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
23751 GACTGCGGGT
*
23761 TGTAACTTGGAGAGGTAGGG-C
1 TGTAACTTGGTGAGGT-GGGAC
* * *
23782 TATAGCTTGGTGATGTGGGAC
1 TGTAACTTGGTGAGGTGGGAC
*
23803 TGTAACTTGGTGAGGTTGGAC
1 TGTAACTTGGTGAGGTGGGAC
23824 TGTA
1 TGTA
23828 CCCAGGAGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 3 0.08
21 34 0.92
ACGTcount: A:0.21, C:0.09, G:0.39, T:0.31
Consensus pattern (21 bp):
TGTAACTTGGTGAGGTGGGAC
Found at i:23877 original size:42 final size:42
Alignment explanation
Indices: 23831--24037 Score: 184
Period size: 42 Copynumber: 4.9 Consensus size: 42
23821 GACTGTACCC
* *
23831 AGGAGAAGTAGGGCTATAAGCGGGTGAAGTAGGGCTGTATGA
1 AGGAGATGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGA
* * * *
23873 AGGAGATGTGGGGCTATAGGAAGGTGAAGTAGGGCTGTACGA
1 AGGAGATGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGA
* * * * *
23915 AGGAGATGTCGGGCTGTATG-ACGGAGATGTAGGGCTGTATGA
1 AGGAGATGTAGGGCTATAAGCA-GGTGAAGTAGGGCTGTATGA
* * * * * * *
23957 TGGAGAAGTGGGGCTATATGCAGGTGAAGTTGGGCTATATGC
1 AGGAGATGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGA
* * * *
23999 TGGTGATGTAGGGCTATATA-CGGGTGAAGTGGGGCTGTA
1 AGGAGATGTAGGGCTATA-AGCAGGTGAAGTAGGGCTGTA
24038 GCTAGGTGAA
Statistics
Matches: 134, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
41 1 0.01
42 132 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.43, T:0.23
Consensus pattern (42 bp):
AGGAGATGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGA
Found at i:23902 original size:63 final size:63
Alignment explanation
Indices: 23831--24016 Score: 192
Period size: 63 Copynumber: 3.0 Consensus size: 63
23821 GACTGTACCC
* *
23831 AGGAGAAGTAGGGCTATAAGCGGGTGAAGTAGGGCTGTATGAAGGAGATGTGGGGCTATAGGA
1 AGGAGAAGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGAAGGAGATGTAGGGCTATAGGA
* * * * * * * * * *
23894 AGGTGAAGTAGGGCTGTACGAAGGAGATGTCGGGCTGTATGACGGAGATGTAGGGCTGTATGA
1 AGGAGAAGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGAAGGAGATGTAGGGCTATAGGA
* * * * * ** *
23957 TGGAGAAGTGGGGCTATATGCAGGTGAAGTTGGGCTATATGCTGGTGATGTAGGGCTATA
1 AGGAGAAGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGAAGGAGATGTAGGGCTATA
24017 TACGGGTGAA
Statistics
Matches: 97, Mismatches: 26, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
63 97 1.00
ACGTcount: A:0.26, C:0.08, G:0.42, T:0.23
Consensus pattern (63 bp):
AGGAGAAGTAGGGCTATAAGCAGGTGAAGTAGGGCTGTATGAAGGAGATGTAGGGCTATAGGA
Found at i:24014 original size:21 final size:21
Alignment explanation
Indices: 23831--24017 Score: 140
Period size: 21 Copynumber: 8.9 Consensus size: 21
23821 GACTGTACCC
* *
23831 AGGAGAAGTAGGGCTATAAGC
1 AGGAGAAGTAGGGCTATATGA
* * *
23852 GGGTGAAGTAGGGCTGTATGA
1 AGGAGAAGTAGGGCTATATGA
* * *
23873 AGGAGATGTGGGGCTATAGGA
1 AGGAGAAGTAGGGCTATATGA
* * *
23894 AGGTGAAGTAGGGCTGTACGA
1 AGGAGAAGTAGGGCTATATGA
* * *
23915 AGGAGATGTCGGGCTGTATGA
1 AGGAGAAGTAGGGCTATATGA
* * *
23936 CGGAGATGTAGGGCTGTATGA
1 AGGAGAAGTAGGGCTATATGA
* * *
23957 TGGAGAAGTGGGGCTATATGC
1 AGGAGAAGTAGGGCTATATGA
* * *
23978 AGGTGAAGTTGGGCTATATGC
1 AGGAGAAGTAGGGCTATATGA
* * *
23999 TGGTGATGTAGGGCTATAT
1 AGGAGAAGTAGGGCTATAT
24018 ACGGGTGAAG
Statistics
Matches: 133, Mismatches: 33, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 133 1.00
ACGTcount: A:0.26, C:0.08, G:0.42, T:0.24
Consensus pattern (21 bp):
AGGAGAAGTAGGGCTATATGA
Found at i:24024 original size:21 final size:21
Alignment explanation
Indices: 23830--24058 Score: 133
Period size: 21 Copynumber: 10.9 Consensus size: 21
23820 GGACTGTACC
* *
23830 CAGGAGAAGTAGGGCTATAAG
1 CAGGTGAAGTAGGGCTATATG
* *
23851 CGGGTGAAGTAGGGCTGTATG
1 CAGGTGAAGTAGGGCTATATG
* * * * *
23872 AAGGAGATGTGGGGCTATAGG
1 CAGGTGAAGTAGGGCTATATG
* * *
23893 AAGGTGAAGTAGGGCTGTACG
1 CAGGTGAAGTAGGGCTATATG
* * * * *
23914 AAGGAGATGTCGGGCTGTATG
1 CAGGTGAAGTAGGGCTATATG
* * *
23935 -ACGGAGATGTAGGGCTGTATG
1 CA-GGTGAAGTAGGGCTATATG
* *
23956 -ATGGAGAAGTGGGGCTATATG
1 CA-GGTGAAGTAGGGCTATATG
*
23977 CAGGTGAAGTTGGGCTATATG
1 CAGGTGAAGTAGGGCTATATG
* * *
23998 CTGGTGATGTAGGGCTATATA
1 CAGGTGAAGTAGGGCTATATG
* * *
24019 CGGGTGAAGTGGGGCTGTA-G
1 CAGGTGAAGTAGGGCTATATG
24039 CTAGGTGAAGT-GGGACTATA
1 C-AGGTGAAGTAGGG-CTATA
24059 GCTGGGGGAT
Statistics
Matches: 166, Mismatches: 38, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
20 5 0.03
21 160 0.96
22 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.42, T:0.23
Consensus pattern (21 bp):
CAGGTGAAGTAGGGCTATATG
Found at i:24133 original size:21 final size:21
Alignment explanation
Indices: 23961--24130 Score: 80
Period size: 21 Copynumber: 8.1 Consensus size: 21
23951 GTATGATGGA
* *
23961 GAAGTGGGGCTATATGC-AGGT
1 GAAGTAGGGCTATA-GCTTGGT
*
23982 GAAGTTGGGCTATATGC-TGGT
1 GAAGTAGGGCTATA-GCTTGGT
* * *
24003 GATGTAGGGCTATATAC-GGGT
1 GAAGTAGGGCTATA-GCTTGGT
* * *
24024 GAAGTGGGGCTGTAGCTAGGT
1 GAAGTAGGGCTATAGCTTGGT
* *
24045 GAAGT-GGGACTATAGCTGGGG
1 GAAGTAGGG-CTATAGCTTGGT
* * * *
24066 GATGT-GGGACTGTAACTTGGA
1 GAAGTAGGG-CTATAGCTTGGT
* * * *
24087 GACGTAGGGCTGTAACTTGGA
1 GAAGTAGGGCTATAGCTTGGT
*
24108 GAGGTAGGGCTATAGCTTGGT
1 GAAGTAGGGCTATAGCTTGGT
24129 GA
1 GA
24131 GGTTGGAGAA
Statistics
Matches: 122, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
20 4 0.03
21 115 0.94
22 3 0.02
ACGTcount: A:0.22, C:0.10, G:0.42, T:0.26
Consensus pattern (21 bp):
GAAGTAGGGCTATAGCTTGGT
Found at i:24244 original size:42 final size:41
Alignment explanation
Indices: 24198--24342 Score: 166
Period size: 42 Copynumber: 3.5 Consensus size: 41
24188 TGGTGAGCTA
** *
24198 GGACTGTAAGTAGGTGATGTGGGGCTGTAACCAGGAGAGGTG
1 GGACTGTAACCAGGTGATGT-GGACTGTAACCAGGAGAGGTG
* * *
24240 GGACTGTACCCAGGAGATGTAGGACTGTAACCAGGAGAGGTA
1 GGACTGTAACCAGGTGATGT-GGACTGTAACCAGGAGAGGTG
* *
24282 GGACTGTAACCAGGTGATGATGGACTGTATCCAGGAGATGATG
1 GGACTGTAACCAGGTGATG-TGGACTGTAACCAGGAGA-GGTG
*
24325 GG-CTGTAACCAGGGGATG
1 GGACTGTAACCAGGTGATG
24343 ACGTAGGAGA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 83 0.94
43 5 0.06
ACGTcount: A:0.27, C:0.14, G:0.39, T:0.20
Consensus pattern (41 bp):
GGACTGTAACCAGGTGATGTGGACTGTAACCAGGAGAGGTG
Found at i:24342 original size:21 final size:21
Alignment explanation
Indices: 24222--24343 Score: 133
Period size: 21 Copynumber: 5.8 Consensus size: 21
24212 TGATGTGGGG
*
24222 CTGTAACCAGGAGA-GGTGGGA
1 CTGTAACCAGGAGATGAT-GGA
*
24243 CTGTACCCAGGAGATG-TAGGA
1 CTGTAACCAGGAGATGAT-GGA
*
24264 CTGTAACCAGGAGA-GGTAGGA
1 CTGTAACCAGGAGATGAT-GGA
*
24285 CTGTAACCAGGTGATGATGGA
1 CTGTAACCAGGAGATGATGGA
* *
24306 CTGTATCCAGGAGATGATGGG
1 CTGTAACCAGGAGATGATGGA
*
24327 CTGTAACCAGGGGATGA
1 CTGTAACCAGGAGATGA
24344 CGTAGGAGAG
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
20 1 0.01
21 84 0.95
22 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.37, T:0.19
Consensus pattern (21 bp):
CTGTAACCAGGAGATGATGGA
Found at i:30822 original size:16 final size:16
Alignment explanation
Indices: 30798--30828 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30788 CAGGATCTAA
30798 TTTTGTCGGAAAGAAT
1 TTTTGTCGGAAAGAAT
*
30814 TTTTTTCGGAAAGAA
1 TTTTGTCGGAAAGAA
30829 GCCCTCCTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (16 bp):
TTTTGTCGGAAAGAAT
Found at i:32435 original size:31 final size:31
Alignment explanation
Indices: 32400--32459 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
32390 TTAAAAAAAT
**
32400 TGACTTAAATAAAAACTTTCGTATAATTCAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
32431 TGACTTAAATAAAAACTTTCAAATAATTC
1 TGACTTAAATAAAAACTTTCAAATAATTC
32460 TCAAATAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAATTCAA
Found at i:34643 original size:19 final size:18
Alignment explanation
Indices: 34619--34665 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
34609 ATATTTAAAA
* *
34619 AATTTTATAATTTTTCTGT
1 AATTTTATAATATTT-TAT
34638 AATTTT-TAATATTTTAT
1 AATTTTATAATATTTTAT
34655 AATTTTTATAA
1 AA-TTTTATAA
34666 GATTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 11 0.46
19 9 0.38
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
AATTTTATAATATTTTAT
Found at i:41758 original size:59 final size:60
Alignment explanation
Indices: 41695--41809 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
41685 AATTCATGTG
41695 CCAAATTGGGTC-AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTA
1 CCAAATTGGGTCAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTA
*
41754 CCAAATTGGGTCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCA
1 CCAAATTGGGTCAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCA
41810 TATTAAGCCT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
59 12 0.22
60 42 0.78
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.23
Consensus pattern (60 bp):
CCAAATTGGGTCAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTA
Found at i:43148 original size:21 final size:19
Alignment explanation
Indices: 43093--43140 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
43083 CATAATATCT
*
43093 AAATACAAAAAAATATCTC
1 AAATACAAAAAAATGTCTC
* *
43112 AAATACATTATAAATGTCTTC
1 AAATACA-AAAAAATGTC-TC
43133 AAATACAA
1 AAATACAA
43141 CAGAAATGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 7 0.30
20 7 0.30
21 9 0.39
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATACAAAAAAATGTCTC
Found at i:43503 original size:37 final size:36
Alignment explanation
Indices: 43458--43576 Score: 99
Period size: 37 Copynumber: 3.4 Consensus size: 36
43448 ATTTTAAGTC
*
43458 ATTCAATTTTCAATATTTACATATTTTATCAATTTA
1 ATTCAATTTTAAATATTTACATATTTTATCAATTTA
* **
43494 ATTCTAATTTTAAATAATT-CAATAAATT-T-AA-TT-
1 ATTC-AATTTTAAATATTTAC-ATATTTTATCAATTTA
** *
43527 ATTCACGTTT--ACATTTACATATTTTATCAATTTA
1 ATTCAATTTTAAATATTTACATATTTTATCAATTTA
43561 ATTCTAATTTTAAATA
1 ATTC-AATTTTAAATA
43577 ATTCAATAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 19
0.65 0.14 0.21
Matches are distributed among these distances:
30 9 0.15
31 2 0.03
32 6 0.10
33 6 0.10
34 6 0.10
35 6 0.10
36 6 0.10
37 19 0.32
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (36 bp):
ATTCAATTTTAAATATTTACATATTTTATCAATTTA
Found at i:43522 original size:30 final size:30
Alignment explanation
Indices: 43488--43593 Score: 86
Period size: 30 Copynumber: 3.3 Consensus size: 30
43478 ATATTTTATC
43488 AATTTAATTCTAATTTTAAATAATTCAATA
1 AATTTAATTCTAATTTTAAATAATTCAATA
* ** * ** *
43518 AATTTAATTATTCACGTTTACATTTACATATTTTATC
1 AATTTAATT-CT-AATTTTA-A---ATA-ATTCAATA
43555 AATTTAATTCTAATTTTAAATAATTCAATA
1 AATTTAATTCTAATTTTAAATAATTCAATA
43585 AATTTAATT
1 AATTTAATT
43594 ATTCACGTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
30 23 0.42
31 3 0.05
32 5 0.09
33 1 0.02
34 1 0.02
35 5 0.09
36 3 0.05
37 14 0.25
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (30 bp):
AATTTAATTCTAATTTTAAATAATTCAATA
Found at i:43549 original size:67 final size:67
Alignment explanation
Indices: 43472--43606 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
43462 AATTTTCAAT
43472 ATTTACATATTTTATCAATTTAATTCTAATTTTAAATAATTCAATAAATTTAATTATTCACGTTT
1 ATTTACATATTTTATCAATTTAATTCTAATTTTAAATAATTCAATAAATTTAATTATTCACGTTT
43537 AC
66 AC
43539 ATTTACATATTTTATCAATTTAATTCTAATTTTAAATAATTCAATAAATTTAATTATTCACGTTT
1 ATTTACATATTTTATCAATTTAATTCTAATTTTAAATAATTCAATAAATTTAATTATTCACGTTT
43604 AC
66 AC
43606 A
1 A
43607 AATTATATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (67 bp):
ATTTACATATTTTATCAATTTAATTCTAATTTTAAATAATTCAATAAATTTAATTATTCACGTTT
AC
Found at i:44768 original size:12 final size:12
Alignment explanation
Indices: 44739--44779 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
44729 AAAAAAAAAT
44739 ATAAATTTAAT-
1 ATAAATTTAATA
*
44750 TTAAATTTAATA
1 ATAAATTTAATA
*
44762 ATAAATTTAAAA
1 ATAAATTTAATA
44774 ATAAAT
1 ATAAAT
44780 AATAAGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAAATTTAATA
Found at i:46301 original size:2 final size:2
Alignment explanation
Indices: 46294--46330 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
46284 ACAATTACAA
*
46294 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.