Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003344.1 Kokia drynarioides strain JFW-HI SEQ_116053, 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: 114773
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:4487 original size:45 final size:46
Alignment explanation
Indices: 4389--4522 Score: 164
Period size: 45 Copynumber: 2.9 Consensus size: 46
4379 TTTATGATTT
* * * *
4389 TTTACCAATATAATACAAAAATAATAATTAAATACCAAAATGAGTTA
1 TTTACCAAAATAGTACAAAAA-AATATTTATATACCAAAATGAGTTA
* *
4436 TTTACCAAAATGGTAC-AAAAAATATTTATATATCAAAAT-AGATTA
1 TTTACCAAAATAGTACAAAAAAATATTTATATACCAAAATGAG-TTA
*
4481 TTTACCAAAATAGTACAAAATAAATATTCATATACCAAAATG
1 TTTACCAAAATAGTACAAAA-AAATATTTATATACCAAAATG
4523 GTATTCACAC
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
44 2 0.03
45 34 0.46
46 7 0.09
47 31 0.42
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (46 bp):
TTTACCAAAATAGTACAAAAAAATATTTATATACCAAAATGAGTTA
Found at i:4633 original size:17 final size:17
Alignment explanation
Indices: 4594--4632 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4584 TATTTTGTAC
* *
4594 CATTCTGATAAATAACT
1 CATTTTGATAAATAAAT
4611 CATTTTGATAAATAAAT
1 CATTTTGATAAATAAAT
4628 -ATTTT
1 CATTTT
4633 TTATATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (17 bp):
CATTTTGATAAATAAAT
Found at i:4746 original size:23 final size:23
Alignment explanation
Indices: 4716--4761 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4706 CTAACAAATT
4716 AATTTAAATTAAAAATAATCAAA
1 AATTTAAATTAAAAATAATCAAA
4739 AATTTAAATTAAAAATAATCAAA
1 AATTTAAATTAAAAATAATCAAA
4762 TTTACCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
AATTTAAATTAAAAATAATCAAA
Found at i:4991 original size:13 final size:12
Alignment explanation
Indices: 4982--5018 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
4972 AATCAATCAC
4982 ATTAAACAATAAA
1 ATTAAACAAT-AA
4995 ATTAAA-AATAA
1 ATTAAACAATAA
5006 ATTAAACAATAA
1 ATTAAACAATAA
5018 A
1 A
5019 CAGAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.35
12 9 0.39
13 6 0.26
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (12 bp):
ATTAAACAATAA
Found at i:5006 original size:12 final size:13
Alignment explanation
Indices: 4982--5018 Score: 60
Period size: 11 Copynumber: 3.0 Consensus size: 13
4972 AATCAATCAC
4982 ATTAAACAATAAA
1 ATTAAACAATAAA
4995 ATTAAA-AAT-AA
1 ATTAAACAATAAA
5006 ATTAAACAATAAA
1 ATTAAACAATAAA
5019 CAGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.36
12 6 0.27
13 8 0.36
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (13 bp):
ATTAAACAATAAA
Found at i:5048 original size:12 final size:12
Alignment explanation
Indices: 5031--5064 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5021 GAAAAAAATA
5031 TCTTTCTCTCTT
1 TCTTTCTCTCTT
*
5043 TCTTTCTTTCTT
1 TCTTTCTCTCTT
*
5055 TCTTTTTCTC
1 TCTTTCTCTC
5065 CCGTTTGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (12 bp):
TCTTTCTCTCTT
Found at i:7569 original size:19 final size:20
Alignment explanation
Indices: 7545--7595 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
7535 ACCATTTTTT
7545 TAATAATTTTTAGAATT-TC
1 TAATAATTTTTAGAATTATC
* *
7564 TAATAATTATTTATAATTATT
1 TAATAATT-TTTAGAATTATC
7585 TAAT-ATTTTTA
1 TAATAATTTTTA
7596 ATAAAAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.43
20 11 0.39
21 5 0.18
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TAATAATTTTTAGAATTATC
Found at i:7597 original size:9 final size:10
Alignment explanation
Indices: 7541--7599 Score: 61
Period size: 10 Copynumber: 6.0 Consensus size: 10
7531 TATTACCATT
7541 TTTTTAATAA
1 TTTTTAATAA
*
7551 TTTTT-AGAA
1 TTTTTAATAA
*
7560 TTTCTAATAA
1 TTTTTAATAA
7570 TTATTT-ATAA
1 TT-TTTAATAA
7580 TTATTTAAT-A
1 TT-TTTAATAA
7590 TTTTTAATAA
1 TTTTTAATAA
7600 AAGTAAGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 13 0.32
10 24 0.59
11 4 0.10
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:28518 original size:36 final size:40
Alignment explanation
Indices: 28478--28559 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
28468 TTTATTTCAT
*
28478 TTATTTT-AA-GTTT-TTTA-TTTTTAATTAATAAATATA
1 TTATTTTCAATGTTTATTTATTTTTTAATAAATAAATATA
* * *
28514 TTATTTTCAATTTTTATTTATTTTTTAATAAATAAATCTT
1 TTATTTTCAATGTTTATTTATTTTTTAATAAATAAATATA
28554 TTATTT
1 TTATTT
28560 ATATAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 7 0.18
37 2 0.05
38 3 0.08
39 4 0.11
40 22 0.58
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (40 bp):
TTATTTTCAATGTTTATTTATTTTTTAATAAATAAATATA
Found at i:28683 original size:19 final size:20
Alignment explanation
Indices: 28649--28696 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
28639 ATAATTTTTT
28649 TATTTATATAAATAAATATA
1 TATTTATATAAATAAATATA
28669 TATTTATAT-AATAAATATA
1 TATTTATATAAATAAATATA
*
28688 TTTTTATAT
1 TATTTATAT
28697 CTATTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTTATATAAATAAATATA
Found at i:28717 original size:4 final size:4
Alignment explanation
Indices: 28708--28732 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28698 TATTTTATAA
28708 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
28733 ATAAAAAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:28726 original size:25 final size:25
Alignment explanation
Indices: 28667--28728 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
28657 TAAATAAATA
*
28667 TATATTTATATAATAAATATATTTT
1 TATATTTATTTAATAAATATATTTT
* * *
28692 TATATCTATTTTATAAATTTATTTAT
1 TATATTTATTTAATAAATATATTT-T
28718 T-TATTTATTTA
1 TATATTTATTTA
28729 TTTAATAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 28 0.93
26 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATTTATTTAATAAATATATTTT
Found at i:30177 original size:9 final size:9
Alignment explanation
Indices: 30163--30187 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30153 TATACTATCA
30163 AATTCTTCC
1 AATTCTTCC
30172 AATTCTTCC
1 AATTCTTCC
30181 AATTCTT
1 AATTCTT
30188 GAGGCATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTCTTCC
Found at i:31312 original size:16 final size:16
Alignment explanation
Indices: 31291--31321 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31281 ATATTTAGTC
31291 ATATAATAAATTATTA
1 ATATAATAAATTATTA
*
31307 ATATAATTAATTATT
1 ATATAATAAATTATT
31322 TTAACAAACT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:31390 original size:16 final size:15
Alignment explanation
Indices: 31350--31390 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31340 TTTCAATTTT
31350 ATTTT-AATAAT-AA
1 ATTTTAAATAATAAA
31363 ATTTTAAA-AATAACA
1 ATTTTAAATAATAA-A
31378 ATTTTAAATAATA
1 ATTTTAAATAATA
31391 TTCAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.33
14 3 0.12
15 9 0.38
16 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:42252 original size:42 final size:42
Alignment explanation
Indices: 42205--42289 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
42195 CACGTAATGT
*
42205 ATTCCTACATACATTATATCTTTATTTCCTAATTTGAGTCTG
1 ATTCCTACATACAGTATATCTTTATTTCCTAATTTGAGTCTG
*
42247 ATTCCTACGTACAGTATATCTTTATTTCCTAATTTGAGTCTG
1 ATTCCTACATACAGTATATCTTTATTTCCTAATTTGAGTCTG
42289 A
1 A
42290 CTTAATCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (42 bp):
ATTCCTACATACAGTATATCTTTATTTCCTAATTTGAGTCTG
Found at i:43914 original size:48 final size:48
Alignment explanation
Indices: 43843--43940 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
43833 AACCCTTTTT
* **
43843 TATCCAATAGTTACAGTAAATCTTAACGAATGACATATTATTAAATGC
1 TATCCAATAGTTACAATAAATCTTAACGAACAACATATTATTAAATGC
** * *
43891 TATCCAATAGTTACAATTGATCTTAATGGACAACATATTATTAAATGC
1 TATCCAATAGTTACAATAAATCTTAACGAACAACATATTATTAAATGC
43939 TA
1 TA
43941 AGGATGGATG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (48 bp):
TATCCAATAGTTACAATAAATCTTAACGAACAACATATTATTAAATGC
Found at i:44794 original size:12 final size:12
Alignment explanation
Indices: 44777--44801 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44767 GCAACAAGAA
44777 ATTTCAAAATAT
1 ATTTCAAAATAT
44789 ATTTCAAAATAT
1 ATTTCAAAATAT
44801 A
1 A
44802 ACAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTCAAAATAT
Found at i:45375 original size:63 final size:62
Alignment explanation
Indices: 45276--45508 Score: 340
Period size: 63 Copynumber: 3.7 Consensus size: 62
45266 ATTTTCGAAA
**
45276 CAGGAGGAGAATCAAATGCCTGCTTTGCAACATCCTTCTGCTCAATGTTCTGTTCATTGGAAG
1 CAGGAGGAGAATCAAATGCCCACTTTGCAACATCCTTCTGCTCAA-GTTCTGTTCATTGGAAG
* *
45339 CAGGAGGAGAATCAAATGCCCACTTCGCAACATCCTTCTGCACCAAGTTCTGTTCATTGGAAG
1 CAGGAGGAGAATCAAATGCCCACTTTGCAACATCCTTCTGC-TCAAGTTCTGTTCATTGGAAG
* * * * * *
45402 GAGGAGGAGAATCAAATGCTCGCTTTGCAACATCCTTCTGTTGCAAGTTATGTTCGTTGGAAG
1 CAGGAGGAGAATCAAATGCCCACTTTGCAACATCCTTCTGCT-CAAGTTCTGTTCATTGGAAG
*
45465 CAGGAGGAGAATCAAATGCCCACTTTGCAACATCCTTCCGCTCA
1 CAGGAGGAGAATCAAATGCCCACTTTGCAACATCCTTCTGCTCA
45509 TAGCTGTGAC
Statistics
Matches: 151, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
62 2 0.01
63 146 0.97
64 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (62 bp):
CAGGAGGAGAATCAAATGCCCACTTTGCAACATCCTTCTGCTCAAGTTCTGTTCATTGGAAG
Found at i:45593 original size:24 final size:24
Alignment explanation
Indices: 45566--45612 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
45556 GCTCCGCCCT
45566 CGACCAGGACTACGGCTGTAGCTA
1 CGACCAGGACTACGGCTGTAGCTA
* *
45590 CGACGAGGGCTACGGCTGTAGCT
1 CGACCAGGACTACGGCTGTAGCT
45613 GCGGCTACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.34, T:0.17
Consensus pattern (24 bp):
CGACCAGGACTACGGCTGTAGCTA
Found at i:45994 original size:18 final size:18
Alignment explanation
Indices: 45973--46030 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
45963 TATCCCTCAT
45973 ACCACCACGACCGCCAAA
1 ACCACCACGACCGCCAAA
* **
45991 ACCACCATC--CC-TC-GT
1 ACCACCA-CGACCGCCAAA
46006 ACCACCACGACCGCCAAA
1 ACCACCACGACCGCCAAA
46024 ACCACCA
1 ACCACCA
46031 TCTCTCATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 3 0.10
17 3 0.10
18 14 0.48
19 1 0.03
ACGTcount: A:0.34, C:0.52, G:0.09, T:0.05
Consensus pattern (18 bp):
ACCACCACGACCGCCAAA
Found at i:46083 original size:33 final size:33
Alignment explanation
Indices: 45948--46080 Score: 176
Period size: 33 Copynumber: 4.0 Consensus size: 33
45938 CTCCCTCCAG
* * *
45948 GACCTCCAAAGCCACTATCCCTCATACCACCAC
1 GACCGCCAAAACCACCATCCCTCATACCACCAC
*
45981 GACCGCCAAAACCACCATCCCTCGTACCACCAC
1 GACCGCCAAAACCACCATCCCTCATACCACCAC
*
46014 GACCGCCAAAACCACCATCTCTCATACCACCAC
1 GACCGCCAAAACCACCATCCCTCATACCACCAC
* * * * *
46047 GGCCACCAAAGCCTCCATCCCTCATTCCACCAC
1 GACCGCCAAAACCACCATCCCTCATACCACCAC
46080 G
1 G
46081 GCCTCCAGAA
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.29, C:0.50, G:0.08, T:0.13
Consensus pattern (33 bp):
GACCGCCAAAACCACCATCCCTCATACCACCAC
Found at i:52967 original size:9 final size:8
Alignment explanation
Indices: 52950--52983 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
52940 AAACGAGGAG
52950 AAGAAAAA
1 AAGAAAAA
*
52958 ATGAAAAA
1 AAGAAAAA
52966 AAGAAAAA
1 AAGAAAAA
52974 AAGAAGAAA
1 AAGAA-AAA
52983 A
1 A
52984 TAAACGAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAGAAAAA
Found at i:55003 original size:25 final size:24
Alignment explanation
Indices: 54954--55002 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
54944 GGTTGAATAA
54954 ATTTTTATACTTTTTAATATTTTT
1 ATTTTTATACTTTTTAATATTTTT
*
54978 ATTTTT-TA-TTTTTAATA-ATTT
1 ATTTTTATACTTTTTAATATTTTT
54999 ATTT
1 ATTT
55003 ACTTTGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 9 0.38
23 2 0.08
24 6 0.25
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTTTTATACTTTTTAATATTTTT
Found at i:56078 original size:13 final size:14
Alignment explanation
Indices: 56060--56093 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
56050 TAAGTTTTTT
56060 TATTTTTAAT-TAA
1 TATTTTTAATATAA
*
56073 TATTTTTAATATAT
1 TATTTTTAATATAA
56087 TATTTTT
1 TATTTTT
56094 TGATTAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTAATATAA
Found at i:56278 original size:15 final size:16
Alignment explanation
Indices: 56249--56281 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
56239 TTATTTTTTT
56249 ATTTTTAATTAATAAA
1 ATTTTTAATTAATAAA
*
56265 ATTTTT-ATTTATAAA
1 ATTTTTAATTAATAAA
56280 AT
1 AT
56282 CAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTTAATTAATAAA
Found at i:56286 original size:20 final size:21
Alignment explanation
Indices: 56244--56286 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
56234 ATATTTTATT
*
56244 TTTTTATTTTTAATTAATAAAA
1 TTTTTATTTATAA-TAATAAAA
*
56266 TTTTTATTTATAA-AATCAAA
1 TTTTTATTTATAATAATAAAA
56286 T
1 T
56287 AATAATATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTTATTTATAATAATAAAA
Found at i:56343 original size:16 final size:16
Alignment explanation
Indices: 56322--56356 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56312 ACATCAACTA
*
56322 ATTCTTTTGATATATT
1 ATTCTTTTGATATAAT
*
56338 ATTCTTTTTATATAAT
1 ATTCTTTTGATATAAT
56354 ATT
1 ATT
56357 TATATGTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (16 bp):
ATTCTTTTGATATAAT
Found at i:59428 original size:52 final size:53
Alignment explanation
Indices: 59359--59505 Score: 170
Period size: 63 Copynumber: 2.6 Consensus size: 53
59349 TTATTTATTT
*
59359 ATTTATTTATCTATATTCAT-AAAATAATAAAACAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAAATAATAAAACAAAATTAATATTATTTTAC
*
59411 ATTTATTTATTTATATTCATACAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAT
1 ATTTATTTATTTATA-T--T-C----AT-AA-AAATAATAAAACAAAATTAATATTATTTTAC
*
59474 ATTTATTTATTTATACTCATAAAAATAATAAA
1 ATTTATTTATTTATATTCATAAAAATAATAAA
59506 TAAATAAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 21
0.77 0.03 0.20
Matches are distributed among these distances:
52 14 0.17
53 11 0.14
54 2 0.02
55 3 0.04
56 1 0.01
59 1 0.01
60 3 0.04
62 1 0.01
63 45 0.56
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (53 bp):
ATTTATTTATTTATATTCATAAAAATAATAAAACAAAATTAATATTATTTTAC
Found at i:59467 original size:63 final size:64
Alignment explanation
Indices: 59380--59512 Score: 232
Period size: 63 Copynumber: 2.1 Consensus size: 64
59370 TATATTCATA
* *
59380 AAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAT-ACAATAATAAAT
1 AAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATACTCATAAAAATAATAAAT
*
59443 AAATAATAAAACAAAATTAATATTATTTTATATTTATTTATTTATACTCATAAAAATAATAAAT
1 AAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATACTCATAAAAATAATAAAT
59507 AAATAA
1 AAATAA
59513 AAATAATAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
63 49 0.74
64 17 0.26
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (64 bp):
AAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATACTCATAAAAATAATAAAT
Found at i:60127 original size:40 final size:38
Alignment explanation
Indices: 60039--60350 Score: 123
Period size: 40 Copynumber: 7.9 Consensus size: 38
60029 CTTTATAATT
* * *
60039 TTAGGGATAAAAGATTGGATTGT-TTCAATCTGCCCCATGG
1 TTAGGG-TAAAAGATCGGA-TGTCTTCAATTTGCCTC-TGG
* * *
60079 -TCGAGGTAAGAGATCGAATGATCTTCAATTTGTCCTCTGG
1 TTAG-GGTAAAAGATCGGATG-TCTTCAATTTG-CCTCTGG
* * *
60119 TTAGGGTAAAAGATTGGAT-TGCTCCAATTTGCCCCATGG
1 TTAGGGTAAAAGATCGGATGT-CTTCAATTTGCCTC-TGG
*** * *
60158 GCGGGGTAAGAGATCGGATGGTCTTCAATCTGCTCTCTGG
1 TTAGGGTAAAAGATCGGAT-GTCTTCAATTTGC-CTCTGG
* * * *
60198 TTAGGGTAAAAGATTGTAT-TGCTTCAATCTGCCCCATGG
1 TTAGGGTAAAAGATCGGATGT-CTTCAATTTGCCTC-TGG
* * * ** *
60237 -TCGAGGTAAGAGATCGAATGGTCTTCAATCTACCCTCTGA
1 TTAG-GGTAAAAGATCGGAT-GTCTTCAAT-TTGCCTCTGG
* * * * *
60277 TCAAGGTAAAAGATTGGATGGTCTTCGATTTACCTCATGG
1 TTAGGGTAAAAGATCGGAT-GTCTTCAATTTGCCTC-TGG
* * *
60317 -TCGAGGTAAGAGATCGGATGGTCTTCAATCTGCC
1 TTAG-GGTAAAAGATCGGAT-GTCTTCAATTTGCC
60351 CATTTCAGCT
Statistics
Matches: 199, Mismatches: 54, Indels: 38
0.68 0.19 0.13
Matches are distributed among these distances:
38 11 0.06
39 69 0.35
40 107 0.54
41 12 0.06
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (38 bp):
TTAGGGTAAAAGATCGGATGTCTTCAATTTGCCTCTGG
Found at i:60135 original size:79 final size:78
Alignment explanation
Indices: 60039--60350 Score: 408
Period size: 79 Copynumber: 3.9 Consensus size: 78
60029 CTTTATAATT
* *
60039 TTAGGGATAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGAGGTAAGAGATCGAATGATCTT
1 TTAGGG-TAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCGAATGGTCTT
*
60104 CAATTTGTCCTCTGG
65 CAATCTG-CCTCTGG
* * * * *
60119 TTAGGGTAAAAGATTGGATTGCTCCAATTTGCCCCATGGGCGGGGTAAGAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCGAATGGTCTTC
60184 AATCTGCTCTCTGG
66 AATCTGC-CTCTGG
*
60198 TTAGGGTAAAAGATTGTATTGCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCGAATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCGAATGGTCTTC
* *
60263 AATCTACCCTCTGA
66 AATCT-GCCTCTGG
* * * * * * * *
60277 TCAAGGTAAAAGATTGGATGGTCTTCGATTTACCTCATGGTCGAGGTAAGAGATCGGATGGTCTT
1 TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCCCATGGTCGAGGTAAGAGATCGAATGGTCTT
60342 CAATCTGCC
65 CAATCTGCC
60351 CATTTCAGCT
Statistics
Matches: 203, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
78 1 0.00
79 151 0.74
80 51 0.25
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (78 bp):
TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCGAATGGTCTTC
AATCTGCCTCTGG
Found at i:60147 original size:39 final size:38
Alignment explanation
Indices: 60039--60230 Score: 127
Period size: 40 Copynumber: 4.9 Consensus size: 38
60029 CTTTATAATT
* * *
60039 TTAGGGATAAAAGATTGGATTGTTTCAATCTGCCCCATGG
1 TTAGGG-TAAAAGATTGGATTGCTTCAATTTGCCTC-TGG
* * * *
60079 -TCGAGGTAAGAGA-TCGAATGATCTTCAATTTGTCCTCTGG
1 TTAG-GGTAAAAGATTGGATTG--CTTCAATTTG-CCTCTGG
* *
60119 TTAGGGTAAAAGATTGGATTGCTCCAATTTGCCCCATGG
1 TTAGGGTAAAAGATTGGATTGCTTCAATTTGCCTC-TGG
*** * * * *
60158 GCGGGGTAAGAGATCGGATGGTCTTCAATCTGCTCTCTGG
1 TTAGGGTAAAAGATTGGATTG-CTTCAATTTGC-CTCTGG
* *
60198 TTAGGGTAAAAGATTGTATTGCTTCAATCTGCC
1 TTAGGGTAAAAGATTGGATTGCTTCAATTTGCC
60231 CCATGGTCGA
Statistics
Matches: 114, Mismatches: 29, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
38 9 0.08
39 46 0.40
40 47 0.41
41 12 0.11
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (38 bp):
TTAGGGTAAAAGATTGGATTGCTTCAATTTGCCTCTGG
Found at i:66237 original size:23 final size:23
Alignment explanation
Indices: 66207--66299 Score: 85
Period size: 23 Copynumber: 4.3 Consensus size: 23
66197 ACACTAGCGC
*
66207 GCTCTCTGTTTAGCA-TTGTGTGT
1 GCTCTCTGATTAGCACTT-TGTGT
66230 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
66253 G--CTC--AGTA-C-C-TTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
66269 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
66292 GCTCTCTG
1 GCTCTCTG
66300 TTACCCAACA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
16 6 0.11
17 1 0.02
18 4 0.07
19 3 0.05
20 2 0.04
21 4 0.07
22 1 0.02
23 33 0.59
24 2 0.04
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:68316 original size:31 final size:31
Alignment explanation
Indices: 68269--68348 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
68259 CGTCTTTCTC
68269 AAACTTT-T-AATGCATGAAAATGCGATGCA
1 AAACTTTATGAATGCATGAAAATGCGATGCA
* * *
68298 AAACTTTATGCATGCATGAAAATGTGATGCG
1 AAACTTTATGAATGCATGAAAATGCGATGCA
* *
68329 GAATTTTATGAATGCATGAA
1 AAACTTTATGAATGCATGAA
68349 TGCATATGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 7 0.16
30 1 0.02
31 35 0.81
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (31 bp):
AAACTTTATGAATGCATGAAAATGCGATGCA
Found at i:70925 original size:67 final size:66
Alignment explanation
Indices: 70821--70977 Score: 225
Period size: 67 Copynumber: 2.4 Consensus size: 66
70811 TTATTTATTT
* * *
70821 ATTTATTTATCTATATTCAT-AA-AAT-AATAAGTAAATAATAAAACAAAATTAATATTATGTTA
1 ATTTATTTATTTATATTCATAAATAATAAATAAATAAATAATAAAACAAAAGTAATATTATGTTA
70883 C
66 C
*
70884 ATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAACAAAAGTAATATTATTTT
1 ATTTATTTATTTATATTCATA-AATAATAAATAAATAAATAATAAAACAAAAGTAATATTATGTT
*
70949 AT
65 AC
70951 ATTTATTTA-TTATATTCATAAA-AATAA
1 ATTTATTTATTTATATTCATAAATAATAA
70978 TAAGAAAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
63 19 0.22
64 5 0.06
65 4 0.05
66 14 0.16
67 43 0.51
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (66 bp):
ATTTATTTATTTATATTCATAAATAATAAATAAATAAATAATAAAACAAAAGTAATATTATGTTA
C
Found at i:72487 original size:3 final size:3
Alignment explanation
Indices: 72479--72505 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
72469 AAAATATTCC
72479 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
72506 GAGAAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:73720 original size:5 final size:5
Alignment explanation
Indices: 73710--73748 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
73700 AAGGAAACTC
73710 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGG
1 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAGG
73749 AAATGGAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (5 bp):
AAGGG
Found at i:81665 original size:20 final size:22
Alignment explanation
Indices: 81626--81676 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
81616 CATTATTGTT
*
81626 TTTTGAATTATTTAATTCAA-A
1 TTTTAAATTATTTAATTCAATA
* *
81647 TTTTAAATT-TTTTATTCAATT
1 TTTTAAATTATTTAATTCAATA
81668 TTTTAAATT
1 TTTTAAATT
81677 GAATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAAATTATTTAATTCAATA
Found at i:98737 original size:20 final size:20
Alignment explanation
Indices: 98710--98748 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
98700 TTTTTAACAC
*
98710 AAATTTTTTAACTTTTATCCA
1 AAATTTTATAA-TTTTATCCA
98731 AAATTTTATAATTTTATC
1 AAATTTTATAATTTTATC
98749 TCAGACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTTTATAATTTTATCCA
Found at i:98903 original size:6 final size:6
Alignment explanation
Indices: 98892--98921 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
98882 GTCGTTGCTC
98892 TGCAAA TGCAAA TGCAAA TGCAAA TGCAAA
1 TGCAAA TGCAAA TGCAAA TGCAAA TGCAAA
98922 AAAAAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
TGCAAA
Found at i:111901 original size:16 final size:16
Alignment explanation
Indices: 111883--111912 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
111873 ACAAAATTAA
111883 AAAAAG-GAAAAAGAG
1 AAAAAGAGAAAAAGAG
111898 AAAAAGAGAAAAAGA
1 AAAAAGAGAAAAAGA
111913 AAAGGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAGAGAAAAAGAG
Found at i:111929 original size:5 final size:5
Alignment explanation
Indices: 111907--111939 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
111897 GAAAAAGAGA
*
111907 AAAAG AAAAG GAAA- AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
111940 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:111929 original size:6 final size:6
Alignment explanation
Indices: 111883--111955 Score: 53
Period size: 6 Copynumber: 12.3 Consensus size: 6
111873 ACAAAATTAA
* * * *
111883 AAAAAGG AAAAAG -AGAA- AAAGAG AAAAAG AAAAGG AAAAAA AGAAAAG
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG
* *
111931 -AAAAG AAAAAT AAAAAT AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AA
111956 GAGGTCGAGG
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
5 10 0.19
6 33 0.63
7 9 0.17
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:112936 original size:50 final size:50
Alignment explanation
Indices: 112873--113049 Score: 214
Period size: 50 Copynumber: 3.5 Consensus size: 50
112863 ATCTTTTACC
* *
112873 CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGAAAATCTCATACA
1 CCTAAAGCTGTAGAGGTGCAGATTGAAACTGTAATGGAAAATCTCATACA
* * * *
112923 CCTAAAGCTGTGGAGGTGCAGATTGAAACCGTAA-CGACAAATATCATACA
1 CCTAAAGCTGTAGAGGTGCAGATTGAAACTGTAATGGA-AAATCTCATACA
* * *
112973 CCTAAAGCTGTAGAGAG-GCAGAATGAAGCTGTAATGGAAAATCTCATTCA
1 CCTAAAGCTGTAGAG-GTGCAGATTGAAACTGTAATGGAAAATCTCATACA
* * *
113023 CTTAAAGCTGTAGAGGAGAAGATTGAA
1 CCTAAAGCTGTAGAGGTGCAGATTGAA
113050 GTCACAAGGA
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
49 3 0.03
50 103 0.94
51 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.21
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGTGCAGATTGAAACTGTAATGGAAAATCTCATACA
Found at i:113242 original size:80 final size:80
Alignment explanation
Indices: 113104--113956 Score: 1147
Period size: 80 Copynumber: 10.7 Consensus size: 80
113094 AGTTACAACC
* * * * *
113104 TCCAGTCTTTTACCCTAACTAAAGGGCAAGATTGAAAATCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
113169 GGCAGATTAAAGAAA
66 GGCAGATTGAAGAAA
* * * *
113184 TCTAATCTTTTATCCTAACTAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
113249 GGTAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * *
113264 TCCAATCTTTTATCCTAATCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCTCGCTCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
113329 GGCAAATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
113344 TCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
113409 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * * * *
113424 TCCAATCTTTTACCCTAACCAGAGGGAAATATTAAAGACCATCTGATCTTTTATCCTGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
113489 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * **
113504 TCCAATTTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATATTTTACCTTGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
* * *
113569 GGTAAATTGAATAAA
66 GGCAGATTGAAGAAA
* * *
113584 TCTAATCTTTTACCTTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGA
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
113649 GGCAGATTGAAAAAA
66 GGCAGATTGAAGAAA
* ** *
113664 TCCAATCTTTTATCCTAATTAGAGGGCAAGATTGAAGACCATTCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
113729 GGCAGATTAAAGAAA
66 GGCAGATTGAAGAAA
* * *
113744 TCCAATCTTTTATCCTAACCAGAGGGCAAGATTGATGACCATCCGATATTTTACCCCGAT-ATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
113808 GGCATATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * * * *
113823 TCTAATCTTCTACCCTAACTAAAGGGCAAGATTGAAGATCATTCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
113888 GACAGATTGAAGAAA
66 GGCAGATTGAAGAAA
** * * * * *
113903 TCCTGTCTTTTACCCCAACTATG-GGG-TAGATTGAAG-CAATCCAATCTTTTACCC
1 TCCAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACCATCCGATCTTTTACCC
113957 TAACTAGAGG
Statistics
Matches: 682, Mismatches: 89, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
78 14 0.02
79 77 0.11
80 591 0.87
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
GGCAGATTGAAGAAA
Found at i:114024 original size:58 final size:58
Alignment explanation
Indices: 113930--114041 Score: 188
Period size: 58 Copynumber: 1.9 Consensus size: 58
113920 ACTATGGGGT
* *
113930 AGATTGAAGCAATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGAC
1 AGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGACTGAAGACCATCCGAC
* *
113988 AGATTGAAGTAATCTAATCTTTTACCCTAACCAGAGGGCAGACTGAAGACCATC
1 AGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGACTGAAGACCATC
114042 AGATCTCTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (58 bp):
AGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGACTGAAGACCATCCGAC
Found at i:114698 original size:17 final size:15
Alignment explanation
Indices: 114676--114711 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
114666 TAAAAAATAA
114676 TATTTATTTTATTATAT
1 TATTTA-TTTATT-TAT
114693 TATTTATTTATTTAT
1 TATTTATTTATTTAT
114708 TATT
1 TATT
114712 GTATGAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 6 0.32
17 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTATTTATTTAT
Found at i:114725 original size:63 final size:66
Alignment explanation
Indices: 114622--114771 Score: 202
Period size: 67 Copynumber: 2.3 Consensus size: 66
114612 TTTCTTCTTC
* *
114622 TTATTAT-TTATTTATTTA-TTATTATTTTTATAAATATAAATAAAT-AA-AAAATAATATTTAT
1 TTATTATATTATTTATTTATTTATTATTTGTATAAATATAAATAAATAAATAAAATAATATTAAT
114683 T
66 T
*
114684 TTATTATATTATTTATTTATTTATTA-TTGTATGAATATAAATAAATAAATGTAAAATAATATTA
1 TTATTATATTATTTATTTATTTATTATTTGTATAAATATAAATAAATAAA--TAAAATAATATTA
114748 ATT
64 ATT
* *
114751 TTGTTTTATTATTTATTTATT
1 TTATTATATTATTTATTTATT
114772 AT
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
62 7 0.09
63 29 0.38
64 8 0.10
67 33 0.43
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (66 bp):
TTATTATATTATTTATTTATTTATTATTTGTATAAATATAAATAAATAAATAAAATAATATTAAT
T
Found at i:114772 original size:63 final size:62
Alignment explanation
Indices: 114626--114773 Score: 178
Period size: 63 Copynumber: 2.4 Consensus size: 62
114616 TTCTTCTTAT
* * *
114626 TATTTATTTATTTA-TTATTATTTTTATAAATATAAATAAATAAAAAATAATATTTATTTTAT
1 TATTTATTTATTTATTTATTA-TTGTATAAATATAAATAAATAAAAAATAATATTAATTTTAG
*
114688 TATATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTTT
1 TAT-TTATTTATTTATTTATTATTGTATAAATATAAATAAAT-AA---AAAATAATATTAATTTT
114753 -G
61 AG
114754 T-TTTA-TTATTTATTTATTAT
1 TATTTATTTATTTATTTATTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
62 3 0.04
63 44 0.58
64 11 0.14
65 1 0.01
66 1 0.01
67 16 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (62 bp):
TATTTATTTATTTATTTATTATTGTATAAATATAAATAAATAAAAAATAATATTAATTTTAG
Done.