Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 24 of 32
Found at i:4098793 original size:34 final size:36
Alignment explanation
Indices: 4098724--4098803 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 36
4098714 ATAATTTAAA
*
4098724 TATATTATAAAATATAATAAAATATAAATATAATATT
1 TATA-TATAAAATATAATAAAATATAAATAAAATATT
4098761 TATATATAAATATATAA-AAAAT-T-AATAAAATATT
1 TATATATAAA-ATATAATAAAATATAAATAAAATATT
* *
4098795 AAAATATAA
1 TATATATAA
4098804 TATTACATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 17 0.44
35 1 0.03
36 11 0.28
37 10 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (36 bp):
TATATATAAAATATAATAAAATATAAATAAAATATT
Found at i:4098795 original size:11 final size:11
Alignment explanation
Indices: 4098720--4098796 Score: 63
Period size: 11 Copynumber: 7.0 Consensus size: 11
4098710 AAAAATAATT
4098720 TAAATATATT-A
1 TAAA-ATATTAA
4098731 TAAAATA-TAA
1 TAAAATATTAA
*
4098741 TAAAATATAAA
1 TAAAATATTAA
*
4098752 TATAATATTTATA
1 TAAAATA-TTA-A
4098765 TATAAATA-T-A
1 TA-AAATATTAA
*
4098775 TAAAAAATTAA
1 TAAAATATTAA
4098786 TAAAATATTAA
1 TAAAATATTAA
4098797 AATATAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
9 5 0.09
10 15 0.28
11 23 0.43
12 3 0.06
13 3 0.06
14 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAAATATTAA
Found at i:4099063 original size:19 final size:18
Alignment explanation
Indices: 4099021--4099063 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
4099011 AAGAACATAT
* *
4099021 AAATTTTTTTATATATTT
1 AAATTTTTTTATAAATTA
*
4099039 AAATTTTATTTTTAAATTA
1 AAATTTT-TTTATAAATTA
4099058 AAATTT
1 AAATTT
4099064 GAATTCATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATTTTTTTATAAATTA
Found at i:4099155 original size:18 final size:18
Alignment explanation
Indices: 4099132--4099170 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4099122 GTTGAAATAA
4099132 AAATTTTAAAATTTAATT
1 AAATTTTAAAATTTAATT
***
4099150 AAATTTTTTTATTTAATT
1 AAATTTTAAAATTTAATT
4099168 AAA
1 AAA
4099171 ATAAATTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTTTAAAATTTAATT
Found at i:4101495 original size:3 final size:3
Alignment explanation
Indices: 4101487--4101539 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
4101477 AAAATTGCAA
*
4101487 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4101535 AAT AA
1 AAT AA
4101540 AAGGAATTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4101830 original size:25 final size:25
Alignment explanation
Indices: 4101792--4101839 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
4101782 TAAATCCTCG
4101792 TTAAAGTTCTTAATAATTTCACAAA
1 TTAAAGTTCTTAATAATTTCACAAA
4101817 TTAAAGTT-TCTAATAATTTCACA
1 TTAAAGTTCT-TAATAATTTCACA
4101840 GATATTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (25 bp):
TTAAAGTTCTTAATAATTTCACAAA
Found at i:4104146 original size:19 final size:17
Alignment explanation
Indices: 4104114--4104149 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
4104104 TTTTTATATA
4104114 AATTTTAATATATTAAT
1 AATTTTAATATATTAAT
4104131 AATTTATAATTATATTAAT
1 AATTT-TAA-TATATTAAT
4104150 TTTAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTAATATATTAAT
Found at i:4104149 original size:16 final size:15
Alignment explanation
Indices: 4104107--4104188 Score: 53
Period size: 16 Copynumber: 5.3 Consensus size: 15
4104097 TATTTTATTT
*
4104107 TTATATAAATTTTAA
1 TTATATTAATTTTAA
*
4104122 TATATTAATAATTTATAA
1 T-TA-TATTAATTT-TAA
4104140 TTATATTAATTTTAA
1 TTATATTAATTTTAA
*
4104155 -AATA-T-ATATTTATA
1 TTATATTAAT-TTTA-A
*
4104169 TCATATTATATTTTAA
1 TTATATTA-ATTTTAA
4104185 TTAT
1 TTAT
4104189 TTTTTTCAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
12 2 0.04
13 5 0.10
14 4 0.08
15 7 0.13
16 15 0.29
17 13 0.25
18 6 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTAATTTTAA
Found at i:4106115 original size:29 final size:29
Alignment explanation
Indices: 4106073--4106135 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
4106063 ATTTAAACGT
* *
4106073 AATTTGGTGGATAGATAATCACATATATA
1 AATTTGGTGCATAGATAATCACATATACA
4106102 AATTTGGTGCATAGATAATCACATATACA
1 AATTTGGTGCATAGATAATCACATATACA
4106131 AATTT
1 AATTT
4106136 TGATGGAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (29 bp):
AATTTGGTGCATAGATAATCACATATACA
Found at i:4124016 original size:28 final size:28
Alignment explanation
Indices: 4123960--4124016 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
4123950 TTAAATTATT
** *
4123960 ATTTAATTAATAAAAATATTTTATTTAA
1 ATTTAATTAATAAAAATATTAAATATAA
4123988 ATTTAATT-ATAAAAATATATAAATATAA
1 ATTTAATTAATAAAAATAT-TAAATATAA
4124016 A
1 A
4124017 ATATAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTTAATTAATAAAAATATTAAATATAA
Found at i:4124041 original size:22 final size:22
Alignment explanation
Indices: 4123980--4124043 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
4123970 TAAAAATATT
4123980 TTATTTAAAT-TTAATTATAAAA
1 TTATTTAAATATTAA-TATAAAA
* * *
4124002 ATATATAAATATAAAATATAAAA
1 TTATTTAAATAT-TAATATAAAA
*
4124025 TTATTTTAATATTAATATA
1 TTATTTAAATATTAATATA
4124044 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 14 0.42
23 17 0.52
24 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATTTAAATATTAATATAAAA
Found at i:4131658 original size:2 final size:2
Alignment explanation
Indices: 4131651--4131680 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4131641 TTATGTTGGT
4131651 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
4131681 ATGTCTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4134985 original size:6 final size:7
Alignment explanation
Indices: 4134929--4134984 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
4134919 TGATATTTAA
4134929 TAAA-TT
1 TAAATTT
4134935 TAAATTT
1 TAAATTT
4134942 TAAATTT
1 TAAATTT
4134949 TAAATTT
1 TAAATTT
4134956 T-AATATT
1 TAAAT-TT
4134963 TATAATTT
1 TA-AATTT
**
4134971 TTTATTT
1 TAAATTT
4134978 TAAATTT
1 TAAATTT
4134985 ATATTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
6 7 0.17
7 29 0.69
8 3 0.07
9 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TAAATTT
Found at i:4134993 original size:22 final size:22
Alignment explanation
Indices: 4134952--4134994 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
4134942 TAAATTTTAA
4134952 ATTTTAATATTTATAATTTTTT
1 ATTTTAATATTTATAATTTTTT
*
4134974 ATTTTAA-ATTTATATTTTTTT
1 ATTTTAATATTTATAATTTTTT
4134995 GGTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTTAATATTTATAATTTTTT
Found at i:4135000 original size:21 final size:21
Alignment explanation
Indices: 4134954--4135002 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4134944 AATTTTAAAT
*
4134954 TTTAATATTTATAATTTTTTAT
1 TTTAA-ATTTATAATTTTTTAG
* *
4134976 TTTAAATTTATATTTTTTTGG
1 TTTAAATTTATAATTTTTTAG
4134997 TTTAAA
1 TTTAAA
4135003 AAATAAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTAAATTTATAATTTTTTAG
Found at i:4135819 original size:16 final size:16
Alignment explanation
Indices: 4135780--4135823 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
4135770 TTATATTAAA
4135780 ATTAAAATATTAAATTT
1 ATTAAAATATT-AATTT
4135797 ATT-AAATATTAATTT
1 ATTAAAATATTAATTT
4135812 -TTAAAAATATTA
1 ATT-AAAATATTA
4135824 CATGTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 5 0.20
16 15 0.60
17 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAAAATATTAATTT
Found at i:4136458 original size:13 final size:14
Alignment explanation
Indices: 4136433--4136469 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
4136423 TTTAATTTTT
4136433 TTATATATTTAAAAA
1 TTATAT-TTTAAAAA
4136448 TT-TATTTT-AAAA
1 TTATATTTTAAAAA
4136460 TTATATTTTA
1 TTATATTTTA
4136470 TATAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 3 0.15
15 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATATTTTAAAAA
Found at i:4139343 original size:15 final size:14
Alignment explanation
Indices: 4139314--4139347 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
4139304 TATTAAATAT
4139314 TAATT-TTTAAAAA
1 TAATTATTTAAAAA
4139327 TAATTATTTATAAAA
1 TAATTATTTA-AAAA
4139342 TAATTA
1 TAATTA
4139348 AATTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 4 0.21
15 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTATTTAAAAA
Found at i:4140506 original size:14 final size:14
Alignment explanation
Indices: 4140487--4140534 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
4140477 TATATATTAA
4140487 ATAAATATTAAAAT
1 ATAAATATTAAAAT
*
4140501 ATAAATATAAAAAT
1 ATAAATATTAAAAT
* *
4140515 ATAATTTTTAAAATT
1 ATAAATATTAAAA-T
4140530 ATAAA
1 ATAAA
4140535 AAATCTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 23 0.82
15 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAAATATTAAAAT
Found at i:4141302 original size:26 final size:26
Alignment explanation
Indices: 4141264--4141337 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 26
4141254 TTTGATCACT
* *
4141264 AAAATTTAAAATTTAATATTTTATAA
1 AAAAATTAAAATTTAAAATTTTATAA
* *
4141290 AAAAATTATAATTTAAAATTTTGT--
1 AAAAATTAAAATTTAAAATTTTATAA
* *
4141314 AAATATTAAAATTT-TAATTTTATA
1 AAAAATTAAAATTTAAAATTTTATA
4141338 TATTAATTAG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 7 0.18
24 12 0.31
26 20 0.51
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
AAAAATTAAAATTTAAAATTTTATAA
Found at i:4141553 original size:2 final size:2
Alignment explanation
Indices: 4141542--4141575 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4141532 ATATTTTGTT
4141542 TA TA -A 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 TA T
4141576 GGTGTTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4142501 original size:2 final size:2
Alignment explanation
Indices: 4142494--4142518 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4142484 ACTTTTCATT
4142494 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
4142519 GCAATGCAAA
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:4142879 original size:2 final size:2
Alignment explanation
Indices: 4142872--4142905 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4142862 ATTATATGAA
* *
4142872 AT AT AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4142906 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4144950 original size:2 final size:2
Alignment explanation
Indices: 4144943--4144971 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4144933 TATTTATGTT
4144943 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 T
4144972 TCATTTAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4149018 original size:28 final size:29
Alignment explanation
Indices: 4148978--4149032 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
4148968 ATTATTTTCC
4148978 GCAATTTTCTAGTTTCATC-TTTCAACCG
1 GCAATTTTCTAGTTTCATCTTTTCAACCG
4149006 GCAATTTTCTAGTTTCATCTTTTCAAC
1 GCAATTTTCTAGTTTCATCTTTTCAAC
4149033 AGACAGGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.45
Consensus pattern (29 bp):
GCAATTTTCTAGTTTCATCTTTTCAACCG
Found at i:4152677 original size:52 final size:52
Alignment explanation
Indices: 4152599--4152703 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
4152589 ACCGTCAGAT
4152599 GGTATAGGACTACATTCAGAATAGCTGTCGTACCAGTACGGAGTCGAAAAAC
1 GGTATAGGACTACATTCAGAATAGCTGTCGTACCAGTACGGAGTCGAAAAAC
*
4152651 GGTATAGGACTACATTCAGAATAGCTGTCGTACCAGTACGGAGTCGAAGAAC
1 GGTATAGGACTACATTCAGAATAGCTGTCGTACCAGTACGGAGTCGAAAAAC
4152703 G
1 G
4152704 CTGTTGCCGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (52 bp):
GGTATAGGACTACATTCAGAATAGCTGTCGTACCAGTACGGAGTCGAAAAAC
Found at i:4153809 original size:2 final size:2
Alignment explanation
Indices: 4153802--4153827 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4153792 TAGTACCTGC
4153802 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4153828 TGGATGAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4156644 original size:92 final size:92
Alignment explanation
Indices: 4156483--4156664 Score: 346
Period size: 92 Copynumber: 2.0 Consensus size: 92
4156473 AAATGAAAGC
4156483 ATCAGCCAGGAAAAATTAAAGTTTACTTTGACCTTCCCTATTCCATCTTAAACCAACAGTAAAAA
1 ATCAGCCAGGAAAAATTAAAGTTTACTTTGACCTTCCCTATTCCATCTTAAACCAACAGTAAAAA
4156548 TCACAAACTTCAACTTGCTATGGGTGA
66 TCACAAACTTCAACTTGCTATGGGTGA
* *
4156575 ATCAGCCAGGCAAAATTAAAGTTTACTTTGACCTTCCCTATTCCATCTTAAACCAACAGTAAAAT
1 ATCAGCCAGGAAAAATTAAAGTTTACTTTGACCTTCCCTATTCCATCTTAAACCAACAGTAAAAA
4156640 TCACAAACTTCAACTTGCTATGGGT
66 TCACAAACTTCAACTTGCTATGGGT
4156665 AAAGTATAGG
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (92 bp):
ATCAGCCAGGAAAAATTAAAGTTTACTTTGACCTTCCCTATTCCATCTTAAACCAACAGTAAAAA
TCACAAACTTCAACTTGCTATGGGTGA
Found at i:4161135 original size:17 final size:17
Alignment explanation
Indices: 4161113--4161168 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
4161103 ATTTCATATT
4161113 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTTTTTTTTC
* *
4161130 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTTTTTTTTC
** * *
4161147 TTCATCTTCTTTCTTTC
1 TTTTTCTTTTTTTTTTC
4161164 TTTTT
1 TTTTT
4161169 TACCTAACCT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTC
Found at i:4161860 original size:18 final size:16
Alignment explanation
Indices: 4161821--4161863 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
4161811 CAGGCCACTC
*
4161821 ATTTTTTTTTTTTTTT
1 ATTTTTTTTTTTTTTG
4161837 ACTTTTTGTTTTCTTTTTG
1 A-TTTTT-TTTT-TTTTTG
4161856 ATTTTTTT
1 ATTTTTTT
4161864 GTTGTTGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 7 0.30
18 9 0.39
19 6 0.26
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.84
Consensus pattern (16 bp):
ATTTTTTTTTTTTTTG
Found at i:4163306 original size:40 final size:40
Alignment explanation
Indices: 4163251--4163369 Score: 215
Period size: 40 Copynumber: 3.0 Consensus size: 40
4163241 AAGAGTAAAG
4163251 TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTTTT
1 TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTTTT
4163291 TGGAAAATAATAAAAGGAATAAATGTTTATATATTC--TT
1 TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTTTT
*
4163329 TGGAAAATAATAAAAGGAATAAATATTTATATATTCTTTT
1 TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTTTT
4163369 T
1 T
4163370 CTTAGATCTC
Statistics
Matches: 76, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
38 37 0.49
40 39 0.51
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (40 bp):
TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTTTT
Found at i:4163331 original size:38 final size:38
Alignment explanation
Indices: 4163251--4163367 Score: 207
Period size: 38 Copynumber: 3.0 Consensus size: 38
4163241 AAGAGTAAAG
4163251 TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTTTT
1 TGGAAAATAATAAAAGGAATAAATGTTTATATATTC--TT
4163291 TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTT
1 TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTT
*
4163329 TGGAAAATAATAAAAGGAATAAATATTTATATATTCTT
1 TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTT
4163367 T
1 T
4163368 TTCTTAGATC
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
38 40 0.53
40 36 0.47
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (38 bp):
TGGAAAATAATAAAAGGAATAAATGTTTATATATTCTT
Found at i:4164223 original size:14 final size:14
Alignment explanation
Indices: 4164197--4164231 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
4164187 ATTTTAACGG
4164197 AAAAAAAAGAATAA
1 AAAAAAAAGAATAA
4164211 AAATAAAAA-AATAA
1 AAA-AAAAAGAATAA
4164225 AAAAAAA
1 AAAAAAA
4164232 TCTGTCAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.09
Consensus pattern (14 bp):
AAAAAAAAGAATAA
Found at i:4165382 original size:17 final size:17
Alignment explanation
Indices: 4165360--4165393 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4165350 CCCAAAGAAG
4165360 AACAA-CACAGAAGCAAA
1 AACAACCACAG-AGCAAA
4165377 AACAACCACAGAGCAAA
1 AACAACCACAGAGCAAA
4165394 TATAGAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.26, G:0.12, T:0.00
Consensus pattern (17 bp):
AACAACCACAGAGCAAA
Found at i:4171708 original size:16 final size:17
Alignment explanation
Indices: 4171687--4171721 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4171677 TTAATTGATA
*
4171687 ATTTAATTA-TAAATAT
1 ATTTAAATATTAAATAT
4171703 ATTTAAATATTAAATAT
1 ATTTAAATATTAAATAT
4171720 AT
1 AT
4171722 AATTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAAATATTAAATAT
Found at i:4171735 original size:20 final size:19
Alignment explanation
Indices: 4171699--4171738 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
4171689 TTAATTATAA
4171699 ATATATTTAAATATTAAAT
1 ATATATTTAAATATTAAAT
* *
4171718 ATATAATTTTAATTTTAAAT
1 ATAT-ATTTAAATATTAAAT
4171738 A
1 A
4171739 ATTATTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATTTAAATATTAAAT
Found at i:4172034 original size:14 final size:14
Alignment explanation
Indices: 4172015--4172054 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
4172005 ATTATTAATT
*
4172015 ATTTTAAATTTTAA
1 ATTTTAAACTTTAA
4172029 ATTTTAAACTTTAA
1 ATTTTAAACTTTAA
*
4172043 GATATTAAACTT
1 -ATTTTAAACTT
4172055 ACTAAAGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTTTAAACTTTAA
Found at i:4172216 original size:3 final size:3
Alignment explanation
Indices: 4172210--4172243 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4172200 AAAAAAAAGG
*
4172210 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4172244 ATACTTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4177277 original size:2 final size:2
Alignment explanation
Indices: 4177270--4177311 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4177260 CCCTCATTAC
4177270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4177312 CTTTAGGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4181587 original size:3 final size:3
Alignment explanation
Indices: 4181579--4181608 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4181569 TATTTATATC
4181579 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4181609 TTGGTTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4184159 original size:20 final size:18
Alignment explanation
Indices: 4184131--4184170 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
4184121 GAGGACTTTT
4184131 AATAAATTTTTATAAGTTTA
1 AATAAATTTTT-TAA-TTTA
*
4184151 AATATATTTTTTAATTTA
1 AATAAATTTTTTAATTTA
4184169 AA
1 AA
4184171 GTGAATTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AATAAATTTTTTAATTTA
Found at i:4185605 original size:19 final size:18
Alignment explanation
Indices: 4185583--4185625 Score: 50
Period size: 22 Copynumber: 2.2 Consensus size: 18
4185573 ATAATTATTT
4185583 TATATTTAAATGCATAAAATA
1 TATATTTAAAT--A-AAAATA
4185604 TAATATTTAAATAAAAATA
1 T-ATATTTAAATAAAAATA
4185623 TAT
1 TAT
4185626 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.10
19 7 0.33
20 1 0.05
21 1 0.05
22 10 0.48
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
TATATTTAAATAAAAATA
Found at i:4185627 original size:16 final size:18
Alignment explanation
Indices: 4185596--4185630 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
4185586 ATTTAAATGC
4185596 ATAAAATATAATATTTAA
1 ATAAAATATAATATTTAA
4185614 ATAAAA-AT-ATATTTAA
1 ATAAAATATAATATTTAA
4185630 A
1 A
4185631 AAATTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 2 0.12
18 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAATATAATATTTAA
Found at i:4185653 original size:24 final size:22
Alignment explanation
Indices: 4185624--4185677 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
4185614 ATAAAAATAT
4185624 ATTTAAAAAATTATTTCTTAAAAA
1 ATTTAAAAAATT-TTT-TTAAAAA
*
4185648 ATTTAATAAATTTTTTTAAAAA
1 ATTTAAAAAATTTTTTTAAAAA
*
4185670 AATTAAAA
1 ATTTAAAA
4185678 TAAAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 13 0.48
23 3 0.11
24 11 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAAAAAATTTTTTTAAAAA
Found at i:4190305 original size:12 final size:12
Alignment explanation
Indices: 4190288--4190312 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4190278 GAGTGGGGGA
4190288 TGTTTTTTTTTT
1 TGTTTTTTTTTT
4190300 TGTTTTTTTTTT
1 TGTTTTTTTTTT
4190312 T
1 T
4190313 TTGGGGGGGG
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TGTTTTTTTTTT
Found at i:4200327 original size:2 final size:2
Alignment explanation
Indices: 4200320--4200361 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4200310 TAAAATGTGT
4200320 TA TA TA TA 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 TA TA TA TA
4200362 CACACACATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4202068 original size:20 final size:19
Alignment explanation
Indices: 4202030--4202097 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
4202020 TAAAATGTAA
*
4202030 TATATATTTAT-ATAAAATT
1 TATATATTAATAAT-AAATT
*
4202049 TAATATATTAATAATTAATTT
1 T-ATATATTAATAA-TAAATT
*
4202070 TATATAATT-TTAATAAATT
1 TATAT-ATTAATAATAAATT
4202089 TATATATTA
1 TATATATTA
4202098 TATTATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
18 3 0.08
19 11 0.28
20 16 0.40
21 9 0.22
22 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATATTAATAATAAATT
Found at i:4202074 original size:40 final size:37
Alignment explanation
Indices: 4202030--4202130 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 37
4202020 TAAAATGTAA
4202030 TATATATTTATATA-AAATTTAATATATTAATAATTAATTT
1 TATATATTTATATATAAATTT-ATATATT-AT-ATT-ATTT
4202070 TATATAATTT-TA-ATAAATTTATATATTATATTATTT
1 TATAT-ATTTATATATAAATTTATATATTATATTATTT
* *
4202106 T-TAT-TTTATAT-TATATTTTTATATT
1 TATATATTTATATATAAATTTATATATT
4202131 TCTATCTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
33 3 0.05
34 14 0.25
35 3 0.05
36 5 0.09
37 3 0.05
38 2 0.04
39 8 0.15
40 13 0.24
41 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (37 bp):
TATATATTTATATATAAATTTATATATTATATTATTT
Found at i:4202946 original size:21 final size:24
Alignment explanation
Indices: 4202903--4202947 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
4202893 TTTTATCATA
4202903 TAAATTATTATTATTAATAAATTT
1 TAAATTATTATTATTAATAAATTT
*
4202927 TAAATT-TT-TTA-TAATTAATTT
1 TAAATTATTATTATTAATAAATTT
4202948 ATATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 3 0.15
23 2 0.10
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TAAATTATTATTATTAATAAATTT
Found at i:4203563 original size:18 final size:19
Alignment explanation
Indices: 4203542--4203587 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
4203532 ATAAATTTAA
* *
4203542 ATTTAATTT-TAAATAATT
1 ATTTAATTTATAAAAAAAT
*
4203560 ATTTTATTTATAAAAAAAT
1 ATTTAATTTATAAAAAAAT
4203579 A-TTAATTTA
1 ATTTAATTTA
4203588 GATTGAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTAATTTATAAAAAAAT
Found at i:4204432 original size:52 final size:52
Alignment explanation
Indices: 4204341--4204443 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
4204331 CTTTCTGGTG
* *
4204341 ACCAAGATTTATGTGGCGAGCACAGGTCTAGTAGTCAGAATGAGTGTTGGCT
1 ACCAAGATTTATGTGACGAGCACAGGTCTAGTAGCCAGAATGAGTGTTGGCT
*
4204393 ACCAGGATTTATGTGACGAGCACAGGTCT-GTTAGCCAGAATGAGTGTTGGC
1 ACCAAGATTTATGTGACGAGCACAGGTCTAG-TAGCCAGAATGAGTGTTGGC
4204444 GATGAGGATA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 1 0.02
52 46 0.98
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (52 bp):
ACCAAGATTTATGTGACGAGCACAGGTCTAGTAGCCAGAATGAGTGTTGGCT
Found at i:4204975 original size:78 final size:78
Alignment explanation
Indices: 4204875--4205104 Score: 273
Period size: 78 Copynumber: 2.9 Consensus size: 78
4204865 GTGGTGGCGA
* * * *
4204875 TCAAGATCGTGGTGTCATGGTGGCGAGTAAGATCGAAGTGACTTGATGTCACTGACAGTTTTGAT
1 TCAAGATCGTGGTGTAATGGTGGCGAGTAAGATCGGAGAGACTTGGTGTCACTGACAGTTTTGAT
4204940 GTCATGGTAGCTA-
66 GTCATGGTAGC-AG
* * *
4204953 TTAGGATCGTGGTGTAATGGTGGCGAGTAAGATTGGAGAGACTTGGTGTCACTGACAGTTTTGAT
1 TCAAGATCGTGGTGTAATGGTGGCGAGTAAGATCGGAGAGACTTGGTGTCACTGACAGTTTTGAT
* * *
4205018 GCCCTGGTGGCAG
66 GTCATGGTAGCAG
* * * * * * * *
4205031 TCAAGATCGCGATGTGATGGTGGCAAGCAGGATCGGAGAGACTTGGTGTCACTGATAGTATTGAT
1 TCAAGATCGTGGTGTAATGGTGGCGAGTAAGATCGGAGAGACTTGGTGTCACTGACAGTTTTGAT
4205096 GTCAGTGGT
66 GTCA-TGGT
4205105 GGCGAGTAGG
Statistics
Matches: 127, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
77 1 0.01
78 122 0.96
79 4 0.03
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.29
Consensus pattern (78 bp):
TCAAGATCGTGGTGTAATGGTGGCGAGTAAGATCGGAGAGACTTGGTGTCACTGACAGTTTTGAT
GTCATGGTAGCAG
Found at i:4205206 original size:132 final size:130
Alignment explanation
Indices: 4205048--4205306 Score: 324
Period size: 130 Copynumber: 2.0 Consensus size: 130
4205038 CGCGATGTGA
* *
4205048 TGGTGGCAAGCAGGATCGGAGAGACTTGGTGTCACTGATAGTATTGATGTCAGTGGTGGCGAGT-
1 TGGTGGCAAGCAGGATCGGAGAGACTTGGTGCCACCGATAGTATTGATG-CAGTGGTGGCGA-TC
* * *
4205112 AGGATCAGGGGTGCCACAGAGGCGAGCATTATTAGACTGCCATGGTGTCACTAAC-GATATTGAT
64 AAGATC-GGAGTGCCACAGAGGCGAGCATGATTAGACTGCCATGGTGTCACTAACAG-TATTGAT
4205176 GTCG
127 GTCG
* * * *
4205180 TGGTGGCAATCAGGATCGGAGTGACTTGGTGCCACCGATAGTATTGATGCTGTGGTGGTGATCAA
1 TGGTGGCAAGCAGGATCGGAGAGACTTGGTGCCACCGATAGTATTGATGCAGTGGTGGCGATCAA
* ** * * * *
4205245 GATCGTAGTGCCATGGTGGCGAGCATGATTAGAGTGTCATGGTGTCACTGACAGTATTGATG
66 GATCGGAGTGCCACAGAGGCGAGCATGATTAGACTGCCATGGTGTCACTAACAGTATTGATG
4205307 CTATAATGGC
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
130 48 0.44
131 16 0.15
132 45 0.41
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.27
Consensus pattern (130 bp):
TGGTGGCAAGCAGGATCGGAGAGACTTGGTGCCACCGATAGTATTGATGCAGTGGTGGCGATCAA
GATCGGAGTGCCACAGAGGCGAGCATGATTAGACTGCCATGGTGTCACTAACAGTATTGATGTCG
Found at i:4205469 original size:26 final size:26
Alignment explanation
Indices: 4205440--4205565 Score: 98
Period size: 26 Copynumber: 4.9 Consensus size: 26
4205430 ATTAATACCG
* *
4205440 TGGTGGCGATCAGGATCGTTGTGCCA
1 TGGTGGCGAGCAGGATCGTAGTGCCA
* * *
4205466 TGGTGGCGAGCATGATCAG-AGTGACT
1 TGGTGGCGAGCAGGATC-GTAGTGCCA
* * * *
4205492 TGGTGCCACTAGCAGTATTG-A-TGCCA
1 TGGTG--GCGAGCAGGATCGTAGTGCCA
*
4205518 TGGTGGCGATCAGGATC-TAGTGCCA
1 TGGTGGCGAGCAGGATCGTAGTGCCA
*
4205543 TGGTGGCGAGCAGGATCGAAGTG
1 TGGTGGCGAGCAGGATCGTAGTG
4205566 GTTTGGTGCC
Statistics
Matches: 75, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
24 8 0.11
25 21 0.28
26 36 0.48
27 3 0.04
28 7 0.09
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (26 bp):
TGGTGGCGAGCAGGATCGTAGTGCCA
Found at i:4205572 original size:77 final size:77
Alignment explanation
Indices: 4205406--4205625 Score: 237
Period size: 77 Copynumber: 2.8 Consensus size: 77
4205396 GGTAGAATTG
* * * * * * * *
4205406 GAGTGACTTAGTGTCACCGATAATATTAATACCGTGGTGGCGATCAGGATCGTTGTGCCATGGTG
1 GAGTGACTTGGTGCCACTGACAGTATTAATGCCATGGTGGCGATCAGGATC-TAGTGCCATGGTG
*
4205471 GCGAGCATGATCA
65 GCGAGCAGGATCA
*
4205484 GAGTGACTTGGTGCCACT-AGCAGTATTGATGCCATGGTGGCGATCAGGATCTAGTGCCATGGTG
1 GAGTGACTTGGTGCCACTGA-CAGTATTAATGCCATGGTGGCGATCAGGATCTAGTGCCATGGTG
4205548 GCGAGCAGGATC-
65 GCGAGCAGGATCA
** * * * * *
4205560 GAAGTGGTTTGGTGCCACTGACAGTATTAATGTCGTGGTGGTGATCACGATTATAGTGCCATGGT
1 G-AGTGACTTGGTGCCACTGACAGTATTAATGCCATGGTGGCGATCAGGA-TCTAGTGCCATGGT
4205625 G
64 G
4205626 TTACTTATAG
Statistics
Matches: 120, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
76 1 0.01
77 63 0.52
78 56 0.47
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.27
Consensus pattern (77 bp):
GAGTGACTTGGTGCCACTGACAGTATTAATGCCATGGTGGCGATCAGGATCTAGTGCCATGGTGG
CGAGCAGGATCA
Found at i:4205671 original size:26 final size:26
Alignment explanation
Indices: 4205642--4205703 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
4205632 ATAGTATTGA
* *
4205642 TGCCAAGGTGGCGATAAGGATCGGAG
1 TGCCAAGGTGACGATAAGAATCGGAG
*
4205668 TGCCAAGGTGACGATCAGAATCGGAG
1 TGCCAAGGTGACGATAAGAATCGGAG
*
4205694 TGCCATGGTG
1 TGCCAAGGTG
4205704 TTACTACAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.39, T:0.18
Consensus pattern (26 bp):
TGCCAAGGTGACGATAAGAATCGGAG
Found at i:4205748 original size:26 final size:26
Alignment explanation
Indices: 4205719--4205771 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
4205709 ACAGTATTGA
4205719 TGCCAAAGTGGTAATCAGAATAAGAG
1 TGCCAAAGTGGTAATCAGAATAAGAG
** * *
4205745 TGCCATTGTGGTAATCAGGATCAGAG
1 TGCCAAAGTGGTAATCAGAATAAGAG
4205771 T
1 T
4205772 AACTCGGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (26 bp):
TGCCAAAGTGGTAATCAGAATAAGAG
Found at i:4205837 original size:52 final size:52
Alignment explanation
Indices: 4205752--4205875 Score: 140
Period size: 52 Copynumber: 2.4 Consensus size: 52
4205742 GAGTGCCATT
* * * * * * **
4205752 GTGGTAATCAGGATCAGAGTAACTCGGTATCACTGACAGTATTAATGCCCTG
1 GTGGCAATCAAGATCGGAGTAACTCGGCATCACTGACAATATTAATACCAAG
* * *
4205804 GTGGCAATCAAGATCGGAGTAACTCGGCGTCACTGACAATATTGATATCAAG
1 GTGGCAATCAAGATCGGAGTAACTCGGCATCACTGACAATATTAATACCAAG
*
4205856 GTGGCGATCAAGATCGGAGT
1 GTGGCAATCAAGATCGGAGT
4205876 GCCATGGTGT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (52 bp):
GTGGCAATCAAGATCGGAGTAACTCGGCATCACTGACAATATTAATACCAAG
Found at i:4205849 original size:207 final size:206
Alignment explanation
Indices: 4205636--4206216 Score: 559
Period size: 207 Copynumber: 2.8 Consensus size: 206
4205626 TTACTTATAG
* * * *
4205636 TATTGATGCCAAGGTGGCGATAAGGATCGGAGTGCCAAGGTGACGATCAGAATCGGAGTGCCATG
1 TATTGATGTCAAGGTGGCGATAAGGATCGGAGTGCCATGGTGACGATCAGAAT-GAAGTGACATG
* *
4205701 GTGTTACTACAGTATTGATGCCAAAGTGGTAATCAGAATAAGAGTGCCATTGTGGTAATCAGGAT
65 GTGTAACTACAGTATTGATGCCAAGGTGGTAATCAGAATAAGAGTGCCATTGTGGTAATCAGGAT
* * ** * * * * *
4205766 CAGAGTAACTCGGTATCACTGACAGTATTAATGCCCTGGTGGCAATCAAGATCGGAGTAACTCGG
130 CAGAGTGACTTGGCGTCACTGACAGTATTGATGCCATGGTGACAATCAAGATCGAAGTAACTCGA
4205831 CGTCACTGACAA
195 CGTCACTGACAA
* * * ** *
4205843 TATTGATATCAAGGTGGCGATCAA-GATCGGAGTGCCATGGTGTTAC-TTACAGTATTTA-TGTC
1 TATTGATGTCAAGGTGGCGAT-AAGGATCGGAGTGCCATGGTG--ACGAT-CAGAATGAAGTGAC
* * * * * *
4205905 A-AG-GTAACGATTAGGATCAGAGTGCCAAGGTGGTAATCAGAATCAGAGTGCCATTGTGGTAAT
62 ATGGTGTAACTA-CAGTAT-TGA-TGCCAAGGTGGTAATCAGAATAAGAGTGCCATTGTGGTAAT
* * * * * *
4205968 CAGGATC-GAGTGACTTGACGTCTCTGACAATATTGATGCCATGGTGACGATCAGGATCGAAGTG
124 CAGGATCAGAGTGACTTGGCGTCACTGACAGTATTGATGCCATGGTGACAATCAAGATCGAAGTA
*
4206032 ACTCGACGTCACTGACAG
189 ACTCGACGTCACTGACAA
* * * *
4206050 TGTTGATGTCAAAGTGGCGATCAGGATCGGAGTGCCATGGT-AGCGATCA-AGATGAAAGTGACT
1 TATTGATGTCAAGGTGGCGATAAGGATCGGAGTGCCATGGTGA-CGATCAGA-ATG-AAGTGACA
* * ** * **
4206113 TGGTGTCACTGACAGTATTGATGCTAAGGTGGCGATCAGGATAAGAGTGCCA-TGATGGCGATCA
63 TGGTGTAACT-ACAGTATTGATGCCAAGGTGGTAATCAGAATAAGAGTGCCATTG-TGGTAATCA
* *
4206177 AGATCAGAGTGACTTGGCGTCATTGACAGTATTGATGCCA
126 GGATCAGAGTGACTTGGCGTCACTGACAGTATTGATGCCA
4206217 AGTATTGTTG
Statistics
Matches: 296, Mismatches: 60, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
204 1 0.00
205 10 0.03
206 10 0.03
207 176 0.59
208 83 0.28
209 15 0.05
210 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (206 bp):
TATTGATGTCAAGGTGGCGATAAGGATCGGAGTGCCATGGTGACGATCAGAATGAAGTGACATGG
TGTAACTACAGTATTGATGCCAAGGTGGTAATCAGAATAAGAGTGCCATTGTGGTAATCAGGATC
AGAGTGACTTGGCGTCACTGACAGTATTGATGCCATGGTGACAATCAAGATCGAAGTAACTCGAC
GTCACTGACAA
Found at i:4205949 original size:26 final size:26
Alignment explanation
Indices: 4205920--4205979 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
4205910 AACGATTAGG
4205920 ATCAGAGTGCCAAGGTGGTAATCAGA
1 ATCAGAGTGCCAAGGTGGTAATCAGA
** *
4205946 ATCAGAGTGCCATTGTGGTAATCAGG
1 ATCAGAGTGCCAAGGTGGTAATCAGA
4205972 ATC-GAGTG
1 ATCAGAGTG
4205980 ACTTGACGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 5 0.16
26 26 0.84
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (26 bp):
ATCAGAGTGCCAAGGTGGTAATCAGA
Found at i:4206047 original size:52 final size:51
Alignment explanation
Indices: 4205966--4206083 Score: 146
Period size: 52 Copynumber: 2.3 Consensus size: 51
4205956 CATTGTGGTA
* * **
4205966 ATCAGGATCGAGTGACTTGACGTCTCTGACAATATTGATGCCATGGTGACG
1 ATCAGGATCGAGTGACTCGACGTCACTGACAATATTGATGCCAAAGTGACG
* * * *
4206017 ATCAGGATCGAAGTGACTCGACGTCACTGACAGTGTTGATGTCAAAGTGGCG
1 ATCAGGATCG-AGTGACTCGACGTCACTGACAATATTGATGCCAAAGTGACG
4206069 ATCAGGATCGGAGTG
1 ATCAGGATC-GAGTG
4206084 CCATGGTAGC
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 10 0.18
52 46 0.81
53 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (51 bp):
ATCAGGATCGAGTGACTCGACGTCACTGACAATATTGATGCCAAAGTGACG
Found at i:4206134 original size:78 final size:77
Alignment explanation
Indices: 4206004--4206214 Score: 255
Period size: 78 Copynumber: 2.7 Consensus size: 77
4205994 ACAATATTGA
* * * *
4206004 TGCCATGGTGACGATCAGGATCG-AAGTGACTCGACGTCACTGACAGTGTTGATG-TCAAAGTGG
1 TGCCATGGTG-CGATCAAGAT-GAAAGTGACTTGGCGTCACTGACAGTATTGATGCT-AAAGTGG
**
4206067 CGATCAGGATCGGAG
63 CGATCAGGATAAGAG
* *
4206082 TGCCATGGTAGCGATCAAGATGAAAGTGACTTGGTGTCACTGACAGTATTGATGCTAAGGTGGCG
1 TGCCATGGT-GCGATCAAGATGAAAGTGACTTGGCGTCACTGACAGTATTGATGCTAAAGTGGCG
4206147 ATCAGGATAAGAG
65 ATCAGGATAAGAG
* * * *
4206160 TGCCATGATGGCGATCAAGATCAGAGTGACTTGGCGTCATTGACAGTATTGATGC
1 TGCCATGGT-GCGATCAAGATGAAAGTGACTTGGCGTCACTGACAGTATTGATGC
4206215 CAAGTATTGT
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
77 1 0.01
78 113 0.97
79 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (77 bp):
TGCCATGGTGCGATCAAGATGAAAGTGACTTGGCGTCACTGACAGTATTGATGCTAAAGTGGCGA
TCAGGATAAGAG
Found at i:4206353 original size:15 final size:16
Alignment explanation
Indices: 4206325--4206355 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4206315 AGCATATTCA
4206325 CGTGAATAAGAGTAAG
1 CGTGAATAAGAGTAAG
4206341 CGTGAAT-AGAGTAAG
1 CGTGAATAAGAGTAAG
4206356 AGTTTCATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.19
Consensus pattern (16 bp):
CGTGAATAAGAGTAAG
Found at i:4208695 original size:98 final size:98
Alignment explanation
Indices: 4208526--4208724 Score: 398
Period size: 98 Copynumber: 2.0 Consensus size: 98
4208516 AAAGGAAGAA
4208526 CGGTGGGAGCATTAGAACAATCATTTGATTTATATCCCAAAATACGCGTTACTACATATTACTGC
1 CGGTGGGAGCATTAGAACAATCATTTGATTTATATCCCAAAATACGCGTTACTACATATTACTGC
4208591 TGTCTTGCAGCGAATTCCACAAGCAATCATAAG
66 TGTCTTGCAGCGAATTCCACAAGCAATCATAAG
4208624 CGGTGGGAGCATTAGAACAATCATTTGATTTATATCCCAAAATACGCGTTACTACATATTACTGC
1 CGGTGGGAGCATTAGAACAATCATTTGATTTATATCCCAAAATACGCGTTACTACATATTACTGC
4208689 TGTCTTGCAGCGAATTCCACAAGCAATCATAAG
66 TGTCTTGCAGCGAATTCCACAAGCAATCATAAG
4208722 CGG
1 CGG
4208725 GCAGCTTGTT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 101 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (98 bp):
CGGTGGGAGCATTAGAACAATCATTTGATTTATATCCCAAAATACGCGTTACTACATATTACTGC
TGTCTTGCAGCGAATTCCACAAGCAATCATAAG
Found at i:4214282 original size:22 final size:22
Alignment explanation
Indices: 4214251--4214293 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4214241 GAATAATTGT
4214251 ATATAATATATAAATTTAAATG
1 ATATAATATATAAATTTAAATG
* *
4214273 ATATATTATATAATTTTAAAT
1 ATATAATATATAAATTTAAAT
4214294 CATTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATAATATATAAATTTAAATG
Found at i:4216813 original size:21 final size:21
Alignment explanation
Indices: 4216787--4216839 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
4216777 ATAATATATA
4216787 TATATATATATACTATATATTTT
1 TATAT-TATAT-CTATATATTTT
*
4216810 TATATTATATTTATATTATTTT
1 TATATTATATCTATA-TATTTT
4216832 T-TATTATA
1 TATATTATA
4216840 ATAATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 11 0.39
22 12 0.43
23 5 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTATATCTATATATTTT
Found at i:4216848 original size:19 final size:22
Alignment explanation
Indices: 4216785--4216848 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 22
4216775 CGATAATATA
4216785 TATATATATATATACTATATATTTT
1 TATAT-TATATATA-TAT-TATTTT
*
4216810 TATATTATATTTATATTATTTT
1 TATATTATATATATATTATTTT
4216832 T-TATTATA-ATA-ATTATT
1 TATATTATATATATATTATT
4216849 AAATTTGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 6 0.16
20 2 0.05
21 7 0.19
22 7 0.19
23 3 0.08
24 7 0.19
25 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TATATTATATATATATTATTTT
Found at i:4216848 original size:22 final size:22
Alignment explanation
Indices: 4216785--4216849 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 22
4216775 CGATAATATA
*
4216785 TATATATATATATACTATATATTTT
1 TATAT-TATA-ATAATAT-TATTTT
* *
4216810 TATATTATATTTATATTATTTT
1 TATATTATAATAATATTATTTT
4216832 T-TATTATAATAATTATTA
1 TATATTATAATAA-TATTA
4216850 AATTTGATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 9 0.26
22 12 0.35
23 4 0.12
24 4 0.12
25 5 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTATAATAATATTATTTT
Found at i:4216895 original size:42 final size:41
Alignment explanation
Indices: 4216815--4216895 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 41
4216805 ATTTTTATAT
* * *
4216815 TATATTTATATTATTTTTTATTATAATAATTATTAAATTTGA
1 TATATTTATATAAATTTTAATTATAATAATTA-TAAATTTGA
4216857 TATATTTATATAAATTTTAATATATAAATAATTA-AAATT
1 TATATTTATATAAATTTTAAT-TAT-AATAATTATAAATT
4216896 ATATAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 23 0.68
43 3 0.09
44 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (41 bp):
TATATTTATATAAATTTTAATTATAATAATTATAAATTTGA
Found at i:4220338 original size:89 final size:89
Alignment explanation
Indices: 4220238--4220423 Score: 372
Period size: 89 Copynumber: 2.1 Consensus size: 89
4220228 TACAAAAAGA
4220238 ATGGCATCGCATGCCGAGCATCATAATTCAATACAAAATTTCTGTTTTTCGTTATACGACCTGAG
1 ATGGCATCGCATGCCGAGCATCATAATTCAATACAAAATTTCTGTTTTTCGTTATACGACCTGAG
4220303 ATAAAGGCCAAAAAAAAAAAAGCC
66 ATAAAGGCCAAAAAAAAAAAAGCC
4220327 ATGGCATCGCATGCCGAGCATCATAATTCAATACAAAATTTCTGTTTTTCGTTATACGACCTGAG
1 ATGGCATCGCATGCCGAGCATCATAATTCAATACAAAATTTCTGTTTTTCGTTATACGACCTGAG
4220392 ATAAAGGCCAAAAAAAAAAAAGCC
66 ATAAAGGCCAAAAAAAAAAAAGCC
4220416 ATGGCATC
1 ATGGCATC
4220424 TTACAAATGA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 97 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (89 bp):
ATGGCATCGCATGCCGAGCATCATAATTCAATACAAAATTTCTGTTTTTCGTTATACGACCTGAG
ATAAAGGCCAAAAAAAAAAAAGCC
Found at i:4223521 original size:20 final size:20
Alignment explanation
Indices: 4223493--4223552 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
4223483 TAATATTTAA
*
4223493 TTATTTATTATTTATTATTT
1 TTATATATTATTTATTATTT
*
4223513 TTATATATT-TTTATAATATT
1 TTATATATTATTTATTAT-TT
*
4223533 TTA-AT-TCTATTTAGTATTT
1 TTATATAT-TATTTATTATTT
4223552 T
1 T
4223553 AAAATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 1 0.03
19 13 0.39
20 19 0.58
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTATATATTATTTATTATTT
Found at i:4223535 original size:10 final size:10
Alignment explanation
Indices: 4223493--4223534 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
4223483 TAATATTTAA
*
4223493 TTATTTATTAT
1 TTATATATT-T
4223504 TTAT-TATTT
1 TTATATATTT
4223513 TTATATATTT
1 TTATATATTT
4223523 TTATAATATTT
1 TTAT-ATATTT
4223534 T
1 T
4223535 AATTCTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.17
10 13 0.45
11 11 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTATATATTT
Found at i:4225126 original size:19 final size:19
Alignment explanation
Indices: 4225102--4225141 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4225092 CTACTTACTT
4225102 TTGTTTGGCTGATGACATG
1 TTGTTTGGCTGATGACATG
4225121 TTGTTTGGCTGATGACATG
1 TTGTTTGGCTGATGACATG
4225140 TT
1 TT
4225142 ATGGTTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.30, T:0.45
Consensus pattern (19 bp):
TTGTTTGGCTGATGACATG
Found at i:4231029 original size:2 final size:2
Alignment explanation
Indices: 4231022--4231048 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4231012 TTCAGGCAAA
4231022 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
4231049 AAAAAAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4231996 original size:29 final size:30
Alignment explanation
Indices: 4231940--4232015 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
4231930 ATTAATAATT
* * *
4231940 TAATATA-TTTTATAATATTTATATTATAA
1 TAATATATTTTTATAAAATATATAATATAA
4231969 TAATATATTTTTATAAAATATA-AATATAA
1 TAATATATTTTTATAAAATATATAATATAA
* * *
4231998 AAATA-ATTTATATTAAAT
1 TAATATATTTTTATAAAAT
4232016 TAATTTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 11 0.28
29 17 0.43
30 12 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAATATATTTTTATAAAATATATAATATAA
Found at i:4232865 original size:19 final size:19
Alignment explanation
Indices: 4232804--4232880 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 19
4232794 ATTAACTAAA
*
4232804 TTTAAAATATTAGAGAATATCT
1 TTTAAAATATTA-TGAAT-T-T
*
4232826 TTTAAAATTTTAAT-ACA-TT
1 TTTAAAATATT-ATGA-ATTT
4232845 TTTAAAATATTATGAATTT
1 TTTAAAATATTATGAATTT
*
4232864 TTTAAAAAATTATGAAT
1 TTTAAAATATTATGAAT
4232881 GCTTGATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.06
19 30 0.64
20 1 0.02
21 1 0.02
22 11 0.23
23 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
TTTAAAATATTATGAATTT
Found at i:4233007 original size:35 final size:37
Alignment explanation
Indices: 4232944--4233014 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 37
4232934 TTTTAAAGTA
* *
4232944 AAAAAATTAACTATTATAATGTTTTTCTTAAATTTTT
1 AAAAAATTAACTATTATAATGATATTCTTAAATTTTT
*
4232981 AAAAAA-TAATTATTATAAT-ATATTCTTAAATTTT
1 AAAAAATTAACTATTATAATGATATTCTTAAATTTT
4233015 ATGAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 13 0.42
36 12 0.39
37 6 0.19
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (37 bp):
AAAAAATTAACTATTATAATGATATTCTTAAATTTTT
Found at i:4233281 original size:2 final size:2
Alignment explanation
Indices: 4233274--4233301 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4233264 CCTTATTTTA
4233274 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4233302 CATTTATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4240029 original size:21 final size:19
Alignment explanation
Indices: 4240005--4240060 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
4239995 TTTACATGTA
4240005 TTTAAAAATAAATTATAAATT
1 TTTAAAAATAAA-TATAAA-T
*
4240026 TTTAAATATATAA-ATAAAT
1 TTTAAAAATA-AATATAAAT
4240045 TTTAAAAATAAATATA
1 TTTAAAAATAAATATA
4240061 TTTGATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 5 0.16
21 9 0.29
22 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAAAATAAATATAAAT
Found at i:4240032 original size:19 final size:21
Alignment explanation
Indices: 4240005--4240058 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
4239995 TTTACATGTA
*
4240005 TTTAAAAATAAAT-TATAAAT
1 TTTAAAAATAAATAAATAAAT
* *
4240025 TTT-TAAATATATAAATAAAT
1 TTTAAAAATAAATAAATAAAT
4240045 TTTAAAAATAAATA
1 TTTAAAAATAAATA
4240059 TATTTGATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 7 0.26
20 12 0.44
21 8 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAAAAATAAATAAATAAAT
Found at i:4240688 original size:28 final size:30
Alignment explanation
Indices: 4240657--4240714 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
4240647 AAATTAATTT
* * *
4240657 AATTTGATT-TAAATTATTATTTTT-TAAA
1 AATTTAATTATAAAATAATATTTTTATAAA
4240685 AATTTAATTATAAAATAATATTTTTATAAA
1 AATTTAATTATAAAATAATATTTTTATAAA
4240715 TAGTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.32
29 13 0.52
30 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
AATTTAATTATAAAATAATATTTTTATAAA
Found at i:4240728 original size:29 final size:29
Alignment explanation
Indices: 4240674--4240729 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
4240664 TTTAAATTAT
* *
4240674 TATTTTTTAAAAATTTAATTATAAAATAA
1 TATTTTTTAAAAAGTTAATTAAAAAATAA
*
4240703 TATTTTTATAAATAGTTAA-TAAAAAAT
1 TATTTTT-TAAAAAGTTAATTAAAAAAT
4240730 TTTAGAATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 14 0.61
30 9 0.39
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
TATTTTTTAAAAAGTTAATTAAAAAATAA
Found at i:4242713 original size:2 final size:2
Alignment explanation
Indices: 4242706--4242749 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4242696 AAGGACCAGG
4242706 TA TA TA TA 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 TA TA TA TA
4242748 TA
1 TA
4242750 ATCTAAAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4247828 original size:14 final size:14
Alignment explanation
Indices: 4247809--4247836 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4247799 ATCGAGTTTG
4247809 CTAGAGTTTACTTT
1 CTAGAGTTTACTTT
4247823 CTAGAGTTTACTTT
1 CTAGAGTTTACTTT
4247837 TAAAATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
CTAGAGTTTACTTT
Found at i:4249625 original size:38 final size:38
Alignment explanation
Indices: 4249547--4249645 Score: 99
Period size: 38 Copynumber: 2.5 Consensus size: 38
4249537 CAACATATTT
* * * **
4249547 AATTTATATTTAATTAATATATTATTTTTTTAATTCAAATA
1 AATTTA-ATTTAATT--TAAATTATTATTTAAATAAAAATA
4249588 AATTTAATTTAATTTAAATTATTATTTAAATAAAAATA
1 AATTTAATTTAATTTAAATTATTATTTAAATAAAAATA
* * *
4249626 TATTTATTTTAATTTTAATT
1 AATTTAATTTAATTTAAATT
4249646 TAATTATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
38 36 0.72
40 8 0.16
41 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (38 bp):
AATTTAATTTAATTTAAATTATTATTTAAATAAAAATA
Found at i:4249647 original size:32 final size:33
Alignment explanation
Indices: 4249574--4249658 Score: 86
Period size: 32 Copynumber: 2.6 Consensus size: 33
4249564 TATATTATTT
* **
4249574 TTTTAATTCAAATAAATTTA-ATTTAATTTAAA
1 TTTTAATTTAAATAAAAATATATTTAATTTAAA
*
4249606 TTATT-ATTTAAATAAAAATATATTT-ATTTTAA
1 TT-TTAATTTAAATAAAAATATATTTAATTTAAA
* *
4249638 TTTTAATTTAATTATAAATAT
1 TTTTAATTTAAATAAAAATAT
4249659 TAATATAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
31 2 0.05
32 36 0.82
33 6 0.14
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTTAATTTAAATAAAAATATATTTAATTTAAA
Found at i:4249651 original size:43 final size:44
Alignment explanation
Indices: 4249590--4249684 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 44
4249580 TTCAAATAAA
*
4249590 TTTAA-TTTAATTTAAATTAT-TAT-TTAAATAAAAATATATTTAT
1 TTTAATTTTAATTTAAATTATAAATATT-AATAAAAA-ATATTTAT
*
4249633 TTTAATTTTAATTT-AATTATAAATATTAATATAAAATATTTAT
1 TTTAATTTTAATTTAAATTATAAATATTAATAAAAAATATTTAT
*
4249676 TTTAGTTTT
1 TTTAATTTT
4249685 TAATATCATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
43 27 0.59
44 17 0.37
45 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (44 bp):
TTTAATTTTAATTTAAATTATAAATATTAATAAAAAATATTTAT
Found at i:4249665 original size:38 final size:38
Alignment explanation
Indices: 4249583--4249657 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
4249573 TTTTTAATTC
* *
4249583 AAATAAATTTAATTTAATTTAAATTATTATTTAAATAA
1 AAATATATTTAATTTAATTTAAATTATAATTTAAATAA
* *
4249621 AAATATATTTATTTTAATTTTAATT-TAATTATAAATA
1 AAATATATTTAATTTAATTTAAATTATAATT-TAAATA
4249658 TTAATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 4 0.12
38 28 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
AAATATATTTAATTTAATTTAAATTATAATTTAAATAA
Found at i:4249700 original size:44 final size:44
Alignment explanation
Indices: 4249616--4249700 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
4249606 TTATTATTTA
*
4249616 AATAAAAATATATTTATTTTAATTTTAATTTAATTATAAATATT
1 AATAAAAATATATTTATTTTAATTTTAATATAATTATAAATATT
* * * *
4249660 AATATAAA-ATATTTATTTTAGTTTTTAATATCATTCTAAAT
1 AATAAAAATATATTTATTTTA-ATTTTAATATAATTATAAAT
4249701 CATGGAACGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 12 0.34
44 23 0.66
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (44 bp):
AATAAAAATATATTTATTTTAATTTTAATATAATTATAAATATT
Found at i:4250469 original size:13 final size:12
Alignment explanation
Indices: 4250448--4250482 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
4250438 CGAAGTAAAC
4250448 AAAAACAAAAAA
1 AAAAACAAAAAA
4250460 AAAAACCAAAAAA
1 AAAAA-CAAAAAA
*
4250473 AAAAGCAAAA
1 AAAAACAAAA
4250483 CCTAGAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAACAAAAAA
Found at i:4250482 original size:11 final size:12
Alignment explanation
Indices: 4250448--4250482 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4250438 CGAAGTAAAC
*
4250448 AAAAACAAAAAA
1 AAAAACCAAAAA
4250460 AAAAACCAAAAA
1 AAAAACCAAAAA
*
4250472 AAAAAGCAAAA
1 AAAAACCAAAA
4250483 CCTAGAAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAACCAAAAA
Found at i:4253012 original size:35 final size:35
Alignment explanation
Indices: 4252966--4253041 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
4252956 TTTTGTTATC
4252966 TAAATGAAATAGATTCGAATCAAATTAATTAAAAT
1 TAAATGAAATAGATTCGAATCAAATTAATTAAAAT
* *
4253001 TAAATGAAATAGATTCGAATTAAATTAATTAAGAT
1 TAAATGAAATAGATTCGAATCAAATTAATTAAAAT
4253036 TAAATG
1 TAAATG
4253042 TAGGATTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.33
Consensus pattern (35 bp):
TAAATGAAATAGATTCGAATCAAATTAATTAAAAT
Found at i:4253021 original size:20 final size:20
Alignment explanation
Indices: 4252966--4253025 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
4252956 TTTTGTTATC
4252966 TAAATGAAATAGATTCGAAT
1 TAAATGAAATAGATTCGAAT
* **
4252986 CAAAT----TA-ATTAAAAT
1 TAAATGAAATAGATTCGAAT
4253001 TAAATGAAATAGATTCGAAT
1 TAAATGAAATAGATTCGAAT
4253021 TAAAT
1 TAAAT
4253026 TAATTAAGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
15 10 0.34
16 2 0.07
19 2 0.07
20 15 0.52
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (20 bp):
TAAATGAAATAGATTCGAAT
Found at i:4253235 original size:17 final size:16
Alignment explanation
Indices: 4253203--4253235 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4253193 TATATTTTTT
*
4253203 TATAAATTTTAATATA
1 TATAAAATTTAATATA
4253219 TATAAAATTTAAT-TA
1 TATAAAATTTAATATA
4253234 TA
1 TA
4253236 AATGCAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAAAATTTAATATA
Found at i:4253289 original size:23 final size:23
Alignment explanation
Indices: 4253263--4253306 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4253253 AATAAGTATG
*
4253263 AATTTTATTTAAAAAATTAATTT
1 AATTATATTTAAAAAATTAATTT
* *
4253286 AATTATATTTAATATATTAAT
1 AATTATATTTAAAAAATTAAT
4253307 AAACATAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTATATTTAAAAAATTAATTT
Found at i:4253846 original size:14 final size:16
Alignment explanation
Indices: 4253823--4253898 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 16
4253813 AAAAAAATTA
*
4253823 TAAATATTAAA-A-AT
1 TAAATTTTAAATATAT
*
4253837 TAAATTTTAAATATGT
1 TAAATTTTAAATATAT
4253853 TAAATTTTATTAATATTAT
1 TAAATTTTA--AATA-TAT
* *
4253872 ATAAA--TTAATTAAAT
1 -TAAATTTTAAATATAT
4253887 TAAATTTTAAAT
1 TAAATTTTAAAT
4253899 TTTTTTAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
14 14 0.29
15 3 0.06
16 18 0.38
18 7 0.15
19 2 0.04
20 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
TAAATTTTAAATATAT
Found at i:4256912 original size:2 final size:2
Alignment explanation
Indices: 4256905--4256939 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4256895 AATTAATCTA
4256905 AT AT AT AT 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 A
4256940 CACACACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4258554 original size:41 final size:41
Alignment explanation
Indices: 4258505--4258587 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 41
4258495 TGCATAAAAA
*
4258505 TTTATAAA-TTTATATATTATAAATA-AAATAA-ATTATATTT
1 TTTATAAATTTTATA-ATAATAAATATAAATAATATTAT-TTT
*
4258545 TTTATTAAATTTTTTAATAATAAATATAAATAATATTATTTT
1 TTTA-TAAATTTTATAATAATAAATATAAATAATATTATTTT
4258587 T
1 T
4258588 AATTAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
40 4 0.11
41 13 0.35
42 15 0.41
43 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
TTTATAAATTTTATAATAATAAATATAAATAATATTATTTT
Found at i:4259746 original size:3 final size:3
Alignment explanation
Indices: 4259738--4259776 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4259728 TTTCTTTTTA
4259738 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4259777 TAATGTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4260493 original size:18 final size:18
Alignment explanation
Indices: 4260470--4260531 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
4260460 TTTTTTAATA
4260470 TAATAATTTATATAAATT
1 TAATAATTTATATAAATT
*
4260488 TAATAAATTA-AT-AATT
1 TAATAATTTATATAAATT
4260504 T-AT--TTTATATAAATT
1 TAATAATTTATATAAATT
4260519 TAA-AATATTATAT
1 TAATAAT-TTATAT
4260532 TATATTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 3 0.08
14 2 0.06
15 7 0.19
16 6 0.17
17 3 0.08
18 15 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTATATAAATT
Found at i:4260521 original size:23 final size:22
Alignment explanation
Indices: 4260486--4260536 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
4260476 TTTATATAAA
4260486 TTTA-ATAAATTAATAAT-TTAT
1 TTTATATAAATTAA-AATATTAT
4260507 TTTATATAAATTTAAAATATTAT
1 TTTATATAAA-TTAAAATATTAT
*
4260530 ATTATAT
1 TTTATAT
4260537 TTTAATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 4 0.15
22 8 0.31
23 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATATAAATTAAAATATTAT
Found at i:4260527 original size:20 final size:20
Alignment explanation
Indices: 4260504--4260553 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 20
4260494 ATTAATAATT
4260504 TATTTTATATAAATTTAAAA
1 TATTTTATATAAATTTAAAA
* * * *
4260524 TATTATAT-TATATTTTAAT
1 TATTTTATATAAATTTAAAA
4260543 TATTTT-TATAA
1 TATTTTATATAA
4260554 TATATTATAC
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTATATAAATTTAAAA
Found at i:4263085 original size:27 final size:27
Alignment explanation
Indices: 4263033--4263085 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
4263023 AATTGACCAT
*
4263033 TAAAATTTTTTTATAATTAAATTTAAA
1 TAAAATTTTTTTATAATTAAAATTAAA
*
4263060 TAAAA-TTTTTTATTATTAATAATTAA
1 TAAAATTTTTTTATAATTAA-AATTAA
4263086 GTACAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TAAAATTTTTTTATAATTAAAATTAAA
Found at i:4263843 original size:21 final size:22
Alignment explanation
Indices: 4263819--4263863 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
4263809 CATATTTAAA
*
4263819 TAAAAATATATAAATATA-ATT
1 TAAAAATATAAAAATATATATT
* *
4263840 TAAAATTTTAAAAATATATATT
1 TAAAAATATAAAAATATATATT
4263862 TA
1 TA
4263864 TATCAAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAATATAAAAATATATATT
Found at i:4263880 original size:17 final size:18
Alignment explanation
Indices: 4263858--4263895 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4263848 TAAAAATATA
*
4263858 TATTTAT-ATCAAACATT
1 TATTTATCATAAAACATT
*
4263875 TATTTATCTTAAAACATT
1 TATTTATCATAAAACATT
4263893 TAT
1 TAT
4263896 CTTCCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTATCATAAAACATT
Found at i:4265110 original size:37 final size:38
Alignment explanation
Indices: 4265048--4265129 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 38
4265038 TGTGTCAGAT
*
4265048 ATATTTAAAAAAATAAATATGAAATATATTT-T-TTAA
1 ATATATAAAAAAATAAATATGAAATATATTTATATTAA
*
4265084 ATATATAAAAAAATTTAAA-ATTAAATATATTTATATTAA
1 ATATATAAAAAAA--TAAATATGAAATATATTTATATTAA
4265123 ATATATA
1 ATATATA
4265130 TGTTTTAAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 12 0.30
37 12 0.30
38 5 0.12
39 11 0.28
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (38 bp):
ATATATAAAAAAATAAATATGAAATATATTTATATTAA
Found at i:4273092 original size:3 final size:3
Alignment explanation
Indices: 4273086--4273115 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4273076 CAAAAAAAAA
4273086 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4273116 CGCTGTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4277110 original size:23 final size:23
Alignment explanation
Indices: 4277080--4277126 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
4277070 GATTTGTTTC
*
4277080 TTTGATCAGATGCTGAATTATTT
1 TTTGATCACATGCTGAATTATTT
4277103 TTTGATCACATGCTGAATTATTT
1 TTTGATCACATGCTGAATTATTT
4277126 T
1 T
4277127 ATCTGCTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.49
Consensus pattern (23 bp):
TTTGATCACATGCTGAATTATTT
Found at i:4277762 original size:12 final size:12
Alignment explanation
Indices: 4277747--4277814 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 12
4277737 GTGGTTTTTG
4277747 ATAATATTTTAT
1 ATAATATTTTAT
4277759 ATAA-A-TTTAT
1 ATAATATTTTAT
*
4277769 -TAATTTTTTAT
1 ATAATATTTTAT
4277780 ATAAT-TTTGATAAT
1 ATAATATTT--T-AT
4277794 ATAATTATTTTA-
1 ATAA-TATTTTAT
4277806 ATAATATTT
1 ATAATATTT
4277815 AATTTTATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 17
0.72 0.02 0.26
Matches are distributed among these distances:
9 3 0.06
10 5 0.11
11 14 0.30
12 12 0.26
13 2 0.04
14 7 0.15
15 1 0.02
16 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (12 bp):
ATAATATTTTAT
Found at i:4277793 original size:21 final size:21
Alignment explanation
Indices: 4277742--4277795 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
4277732 GTTTGGTGGT
4277742 TTTTGATAATATTTTATATAA
1 TTTTGATAATATTTTATATAA
* *
4277763 ATTT-ATTAATTTTTTATATAA
1 TTTTGA-TAATATTTTATATAA
4277784 TTTTGATAATAT
1 TTTTGATAATAT
4277796 AATTATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTTGATAATATTTTATATAA
Found at i:4278320 original size:20 final size:20
Alignment explanation
Indices: 4278296--4278350 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
4278286 TTTTTAATAA
*
4278296 AAATTTTAATAATTTAAATT
1 AAATTTAAATAATTTAAATT
* * * *
4278316 GAATTTGATTAATTTAATTT
1 AAATTTAAATAATTTAAATT
4278336 AAATTTAAATAATTT
1 AAATTTAAATAATTT
4278351 TTTTTAAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
AAATTTAAATAATTTAAATT
Found at i:4278571 original size:2 final size:2
Alignment explanation
Indices: 4278556--4278595 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4278546 TTAAACCGAA
* * *
4278556 AT AT AT AG AC AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4278596 GCCATACAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4279382 original size:18 final size:18
Alignment explanation
Indices: 4279332--4279383 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
4279322 ATTTAAATAA
*
4279332 ATATTAATATTATAATTTTT
1 ATATTAATATAAT-A-TTTT
* *
4279352 AAATAAATA-AATATTTT
1 ATATTAATATAATATTTT
4279369 ATATTAATATAATAT
1 ATATTAATATAATAT
4279384 ATAAAATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 11 0.42
18 6 0.23
19 2 0.08
20 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTAATATAATATTTT
Found at i:4281804 original size:19 final size:19
Alignment explanation
Indices: 4281777--4281843 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
4281767 CAGTAGCTAA
*
4281777 TTATGTATCGATACAACAC
1 TTATATATCGATACAACAC
4281796 TTATATATCGAT---ACA-
1 TTATATATCGATACAACAC
4281811 -T-TATATCGATACAACAC
1 TTATATATCGATACAACAC
*
4281828 TTATGTATCGATACAA
1 TTATATATCGATACAA
4281844 ATCGTTGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
16 6 0.15
18 1 0.03
19 23 0.57
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (19 bp):
TTATATATCGATACAACAC
Found at i:4281817 original size:13 final size:13
Alignment explanation
Indices: 4281799--4281823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4281789 ACAACACTTA
4281799 TATATCGATACAT
1 TATATCGATACAT
4281812 TATATCGATACA
1 TATATCGATACA
4281824 ACACTTATGT
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:4281823 original size:32 final size:32
Alignment explanation
Indices: 4281782--4281842 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
4281772 GCTAATTATG
4281782 TATCGATACAACACTTATATATCGATACATTA
1 TATCGATACAACACTTATATATCGATACATTA
*
4281814 TATCGATACAACACTTATGTATCGATACA
1 TATCGATACAACACTTATATATCGATACA
4281843 AATCGTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (32 bp):
TATCGATACAACACTTATATATCGATACATTA
Found at i:4283687 original size:17 final size:17
Alignment explanation
Indices: 4283642--4283702 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
4283632 ATTTGTAATT
*
4283642 AAATTTATTTAATGAATAA
1 AAATTTA-TTAAT-AAAAA
*
4283661 ATATTT-TTAATAAAAA
1 AAATTTATTAATAAAAA
* *
4283677 AAATTTATTAACAAATA
1 AAATTTATTAATAAAAA
*
4283694 AATTTTATT
1 AAATTTATT
4283703 GATCAAGTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 9 0.26
17 21 0.60
19 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AAATTTATTAATAAAAA
Found at i:4286003 original size:17 final size:19
Alignment explanation
Indices: 4285972--4286022 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
4285962 TAGTTAAATA
4285972 TAAATATAATATAAATTAT
1 TAAATATAATATAAATTAT
*
4285991 TAAATAT-AT-TAAATTTT
1 TAAATATAATATAAATTAT
*
4286008 TAAAAATAAATATAA
1 TAAATAT-AATATAA
4286023 TATATTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 13 0.48
18 2 0.07
19 9 0.33
20 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATATAATATAAATTAT
Found at i:4291522 original size:20 final size:20
Alignment explanation
Indices: 4291485--4291523 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4291475 GGATTTTTGA
* * *
4291485 TGCTCTCTACAGACAGTAAG
1 TGCTCCCTACAAAAAGTAAG
4291505 TGCTCCCTACAAAAAGTAA
1 TGCTCCCTACAAAAAGTAA
4291524 CAGAGTCCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (20 bp):
TGCTCCCTACAAAAAGTAAG
Found at i:4294433 original size:2 final size:2
Alignment explanation
Indices: 4294426--4294464 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4294416 TATGTTACAT
4294426 TA TA TA 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 TA TA TA T
4294465 TTGTTAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.