Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 175 of 204
Found at i:52220750 original size:35 final size:35
Alignment explanation
Indices: 52220710--52220776 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
52220700 TAATTTTTAA
*
52220710 TGTAATATACTATTTTAATATGCTGTTATAAAATT
1 TGTAATATACTATTTTAATATACTGTTATAAAATT
* *
52220745 TGTAATATTCTGTTTTAATATACTGTTATAAA
1 TGTAATATACTATTTTAATATACTGTTATAAA
52220777 TATATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (35 bp):
TGTAATATACTATTTTAATATACTGTTATAAAATT
Found at i:52220841 original size:53 final size:54
Alignment explanation
Indices: 52220761--52220871 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 54
52220751 ATTCTGTTTT
* * * *
52220761 AATATACTGTTATAAATATATTATTTTAATATACTGTTTTAGTATATTGTTATA
1 AATATACTATTATAAATATAATATTTTAATATACTGTTTTAATATATCGTTATA
* * *
52220815 AATATACTATT-TTAATATAATGTTTTAATATATTGTTTTAATATATCGTTATA
1 AATATACTATTATAAATATAATATTTTAATATACTGTTTTAATATATCGTTATA
52220868 AATA
1 AATA
52220872 CTACACCTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 40 0.80
54 10 0.20
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (54 bp):
AATATACTATTATAAATATAATATTTTAATATACTGTTTTAATATATCGTTATA
Found at i:52220883 original size:53 final size:53
Alignment explanation
Indices: 52220775--52220911 Score: 152
Period size: 53 Copynumber: 2.6 Consensus size: 53
52220765 TACTGTTATA
* * * **
52220775 AATATATTATTTTAATATACTGTTTTAGTATATTGTTATAAATATACTATTTT
1 AATATAATATTTTAATATACTGTTTTAATATATCGTTATAAATATACTACCTT
* *
52220828 AATATAATGTTTTAATATATTGTTTTAATATATCGTTATAAATACTAC-ACCTT
1 AATATAATATTTTAATATACTGTTTTAATATATCGTTATAAATA-TACTACCTT
** * *
52220881 AAT-TTTTAATATAATATACTGTTTTAATATA
1 AATATAATATTTTAATATACTGTTTTAATATA
52220912 CTATTATAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
52 22 0.31
53 45 0.64
54 3 0.04
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (53 bp):
AATATAATATTTTAATATACTGTTTTAATATATCGTTATAAATATACTACCTT
Found at i:52220961 original size:81 final size:81
Alignment explanation
Indices: 52220863--52221023 Score: 277
Period size: 81 Copynumber: 2.0 Consensus size: 81
52220853 TAATATATCG
*
52220863 TTATAAATACTACACCTTAATTTTTAATATAATATACTGTTTTAATATACTATTATAAAATTTGT
1 TTATAAATACTACACCTTAATTATTAATATAATATACTGTTTTAATATACTATTATAAAATTTGT
*
52220928 AATATATTGTTATAAC
66 AATATACTGTTATAAC
* * *
52220944 TTATAAATACTACACCTTAATTATTATTGTAATATACTGTTTTAATATACTGTTATAAAATTTGT
1 TTATAAATACTACACCTTAATTATTAATATAATATACTGTTTTAATATACTATTATAAAATTTGT
52221009 AATATACTGTTATAA
66 AATATACTGTTATAA
52221024 ATATACTATT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (81 bp):
TTATAAATACTACACCTTAATTATTAATATAATATACTGTTTTAATATACTATTATAAAATTTGT
AATATACTGTTATAAC
Found at i:52220991 original size:13 final size:13
Alignment explanation
Indices: 52220973--52221035 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
52220963 ATTATTATTG
52220973 TAATATACTGTTT
1 TAATATACTGTTT
*
52220986 TAATATACTGTTA
1 TAATATACTGTTT
*
52220999 TAA-A-A-T-TTG
1 TAATATACTGTTT
52221008 TAATATACTGTTAT
1 TAATATACTGTT-T
* *
52221022 AAATATACTATTT
1 TAATATACTGTTT
52221035 T
1 T
52221036 TAAAACGGGC
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
9 5 0.13
10 2 0.05
11 2 0.05
12 2 0.05
13 18 0.46
14 10 0.26
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:52222114 original size:26 final size:27
Alignment explanation
Indices: 52222063--52222125 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
52222053 CATGTTAAAT
52222063 ATATATATTTGATTAAAAAATAAAAAA
1 ATATATATTTGATTAAAAAATAAAAAA
52222090 ATATATATTTGATT-AAAAATAAAAAA
1 ATATATATTTGATTAAAAAATAAAAAA
52222116 ATATATATTT
1 ATATATATTT
52222126 AATATATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (27 bp):
ATATATATTTGATTAAAAAATAAAAAA
Found at i:52222527 original size:16 final size:13
Alignment explanation
Indices: 52222504--52222552 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
52222494 GAGCAATTTA
52222504 ATTTTTTTCTCTTT
1 ATTTTTTT-TCTTT
*
52222518 ATGTTATTTTAACTTT
1 AT-TT-TTTT-TCTTT
52222534 ATTTTTTTTCTTT
1 ATTTTTTTTCTTT
52222547 ATTTTT
1 ATTTTT
52222553 CATTCTCTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 10 0.33
14 6 0.20
15 4 0.13
16 10 0.33
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (13 bp):
ATTTTTTTTCTTT
Found at i:52223089 original size:3 final size:3
Alignment explanation
Indices: 52223081--52223120 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
52223071 TCTATGCTGA
52223081 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
52223121 CAAATTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:52228618 original size:31 final size:31
Alignment explanation
Indices: 52228583--52228641 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
52228573 CTTAACAGTC
*
52228583 TAGTGACTTAAATAAAAACTTTTGAATATTT
1 TAGTGACTTAAATAAAAACTTTCGAATATTT
52228614 TAGTGACTTAAATAAAAACTTTCGAATA
1 TAGTGACTTAAATAAAAACTTTCGAATA
52228642 GTTCAATGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTCGAATATTT
Found at i:52228934 original size:6 final size:6
Alignment explanation
Indices: 52228923--52228948 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52228913 TCAATAAAAA
52228923 GCCTCG GCCTCG GCCTCG GCCTCG GC
1 GCCTCG GCCTCG GCCTCG GCCTCG GC
52228949 GTTGTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.35, T:0.15
Consensus pattern (6 bp):
GCCTCG
Found at i:52228958 original size:6 final size:6
Alignment explanation
Indices: 52228949--52228983 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
52228939 CGGCCTCGGC
*
52228949 GTTGTT GTTGTG GTTGTG GTTGTG GTTGTG GTTGT
1 GTTGTG GTTGTG GTTGTG GTTGTG GTTGTG GTTGT
52228984 AGATCTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (6 bp):
GTTGTG
Found at i:52244139 original size:2 final size:2
Alignment explanation
Indices: 52244132--52244163 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52244122 GTGGGTAATA
52244132 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
52244164 GGTGTGTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52250562 original size:9 final size:9
Alignment explanation
Indices: 52250486--52250564 Score: 51
Period size: 9 Copynumber: 8.7 Consensus size: 9
52250476 AAAAATATTT
52250486 TATTTT-TA
1 TATTTTATA
52250494 T-TTTTATAA
1 TATTTTAT-A
52250503 CTATTATTATA
1 -TATT-TTATA
*
52250514 TATATTA-A
1 TATTTTATA
52250522 -ATTTTATA
1 TATTTTATA
*
52250530 TGCTTTTATAA
1 T-ATTTTAT-A
52250541 TATTTTA-A
1 TATTTTATA
52250549 CTATTTTATA
1 -TATTTTATA
52250559 TATTTT
1 TATTTT
52250565 TAATTAGATG
Statistics
Matches: 56, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
7 9 0.16
8 5 0.09
9 17 0.30
10 16 0.29
11 5 0.09
12 4 0.07
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (9 bp):
TATTTTATA
Found at i:52250994 original size:3 final size:3
Alignment explanation
Indices: 52250986--52251017 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
52250976 TTTAGATTTG
52250986 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52251018 CATTGACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52253884 original size:3 final size:3
Alignment explanation
Indices: 52253872--52253927 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
52253862 TTAATTCTTC
*
52253872 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52253920 TAT ATAT T
1 TAT -TAT T
52253928 TTAATTGGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:52254560 original size:25 final size:25
Alignment explanation
Indices: 52254525--52254582 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
52254515 TATATATTAA
*
52254525 ATATATATTTTATTTTTAATCAAAT
1 ATATATTTTTTATTTTTAATCAAAT
*
52254550 ATATATTTTTTATTTTTAATTAAAT
1 ATATATTTTTTATTTTTAATCAAAT
52254575 ATATATTT
1 ATATATTT
52254583 AATATGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
ATATATTTTTTATTTTTAATCAAAT
Found at i:52255816 original size:25 final size:25
Alignment explanation
Indices: 52255788--52255853 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
52255778 CTAATATTTA
*
52255788 GCTCTCACGAGCTTCCCGATTAATG
1 GCTCTCATGAGCTTCCCGATTAATG
* *
52255813 GCTCTCTTGAGCTTCCCGATTTATG
1 GCTCTCATGAGCTTCCCGATTAATG
*
52255838 GCTCGCATGAGCTTCC
1 GCTCTCATGAGCTTCC
52255854 TGATGTACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.15, C:0.32, G:0.21, T:0.32
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATTAATG
Found at i:52255867 original size:25 final size:26
Alignment explanation
Indices: 52255839--52255903 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 26
52255829 CGATTTATGG
*
52255839 CTCGCATGAGCTTCCT-GATGTACAA
1 CTCGCATGAGCTTCCTCGATATACAA
** * *
52255864 CTCGGTTGAGCTT-CTCGTTATACAG
1 CTCGCATGAGCTTCCTCGATATACAA
*
52255889 CTCACATGAGCTTCC
1 CTCGCATGAGCTTCC
52255904 CGTTTACATG
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
24 2 0.07
25 27 0.90
26 1 0.03
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (26 bp):
CTCGCATGAGCTTCCTCGATATACAA
Found at i:52255907 original size:25 final size:25
Alignment explanation
Indices: 52255870--52255924 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
52255860 ACAACTCGGT
*
52255870 TGAGCTTCTCGTTATACA-GCTC-ACA
1 TGAGCTTCCCGTT-TACATGCTCGA-A
52255895 TGAGCTTCCCGTTTACATGCTCGAA
1 TGAGCTTCCCGTTTACATGCTCGAA
52255920 TGAGC
1 TGAGC
52255925 ATTCTTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 4 0.15
25 22 0.81
26 1 0.04
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (25 bp):
TGAGCTTCCCGTTTACATGCTCGAA
Found at i:52268245 original size:9 final size:9
Alignment explanation
Indices: 52268218--52268254 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
52268208 TGAGTTTTCG
52268218 AATTCGAAT
1 AATTCGAAT
* *
52268227 AACTCAAAT
1 AATTCGAAT
52268236 AATTCGAAT
1 AATTCGAAT
52268245 AATTCGAAT
1 AATTCGAAT
52268254 A
1 A
52268255 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52271201 original size:19 final size:19
Alignment explanation
Indices: 52271177--52271280 Score: 68
Period size: 19 Copynumber: 5.1 Consensus size: 19
52271167 AAAATTATTA
52271177 TTTTATAAAATTTTAAATT
1 TTTTATAAAATTTTAAATT
* * *
52271196 TTTTATATATTTTTAGATT
1 TTTTATAAAATTTTAAATT
* *
52271215 TTTT-TTAAATTTATAATTTT
1 TTTTATAAAATTT-TAA-ATT
52271235 TGTTTAAAATAAAAATTTTAGAA-T
1 T-TTT---AT-AAAATTTTA-AATT
52271259 TTTTATAAATATTTTAAATT
1 TTTTATAAA-ATTTTAAATT
52271279 TT
1 TT
52271281 AAAAATTACT
Statistics
Matches: 64, Mismatches: 10, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
18 5 0.08
19 27 0.42
20 14 0.22
21 3 0.05
23 3 0.05
24 2 0.03
25 3 0.05
26 7 0.11
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTTATAAAATTTTAAATT
Found at i:52271281 original size:18 final size:20
Alignment explanation
Indices: 52271243--52271280 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52271233 TTTGTTTAAA
*
52271243 ATAAAAATTTTAGAATTTTT
1 ATAAATATTTTAGAATTTTT
52271263 ATAAATATTTTA-AATTTT
1 ATAAATATTTTAGAATTTT
52271281 AAAAATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAGAATTTTT
Found at i:52271286 original size:18 final size:20
Alignment explanation
Indices: 52271245--52271286 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
52271235 TGTTTAAAAT
52271245 AAAA-ATTTTAGAATTTTTA
1 AAAATATTTTAGAATTTTTA
*
52271264 TAAATATTTTA-AA-TTTTA
1 AAAATATTTTAGAATTTTTA
52271282 AAAAT
1 AAAAT
52271287 TACTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 9 0.45
19 5 0.25
20 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATATTTTAGAATTTTTA
Found at i:52275742 original size:24 final size:24
Alignment explanation
Indices: 52275710--52275756 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
52275700 GACAAAAAAA
52275710 AATGTTGTATGTAAATAAATGATG
1 AATGTTGTATGTAAATAAATGATG
*
52275734 AATGTTGTATTTAAATAAATGAT
1 AATGTTGTATGTAAATAAATGAT
52275757 CTCGGCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (24 bp):
AATGTTGTATGTAAATAAATGATG
Found at i:52278614 original size:12 final size:12
Alignment explanation
Indices: 52278597--52278634 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
52278587 GAAGCCAGAA
52278597 CCGGAGCTGGAG
1 CCGGAGCTGGAG
* *
52278609 CCGGAGCCGGAT
1 CCGGAGCTGGAG
52278621 CCGGAGCTGGAG
1 CCGGAGCTGGAG
52278633 CC
1 CC
52278635 ACTGCTTCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.16, C:0.32, G:0.45, T:0.08
Consensus pattern (12 bp):
CCGGAGCTGGAG
Found at i:52278616 original size:24 final size:24
Alignment explanation
Indices: 52278589--52278634 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
52278579 GATCAAGCGA
52278589 AGCCAGAACCGGAGCTGGAGCCGG
1 AGCCAGAACCGGAGCTGGAGCCGG
* *
52278613 AGCCGGATCCGGAGCTGGAGCC
1 AGCCAGAACCGGAGCTGGAGCC
52278635 ACTGCTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.30, G:0.41, T:0.07
Consensus pattern (24 bp):
AGCCAGAACCGGAGCTGGAGCCGG
Found at i:52279777 original size:11 final size:10
Alignment explanation
Indices: 52279730--52279777 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
52279720 AAAAAATTAG
*
52279730 GGAAAAAAGA
1 GGAAAGAAGA
52279740 GGGAAAGAAGA
1 -GGAAAGAAGA
*
52279751 GGAAAGATGA
1 GGAAAGAAGA
52279761 -GAAAGAAGAA
1 GGAAAGAAG-A
52279771 GGAAAGA
1 GGAAAGA
52279778 TATGCAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 7 0.22
10 10 0.31
11 15 0.47
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (10 bp):
GGAAAGAAGA
Found at i:52286147 original size:21 final size:21
Alignment explanation
Indices: 52286109--52286148 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52286099 CCCTGAACCC
*
52286109 GTTTAAGGTTCGAGGTTCAGT
1 GTTTAAGGTTCGAAGTTCAGT
* *
52286130 GTTTAATGTTTGAAGTTCA
1 GTTTAAGGTTCGAAGTTCA
52286149 TGATTCAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (21 bp):
GTTTAAGGTTCGAAGTTCAGT
Found at i:52286727 original size:24 final size:26
Alignment explanation
Indices: 52286680--52286727 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
52286670 ATGATTATAA
* *
52286680 TAAAATATTTAGTATTTTATAAATCC
1 TAAAATATTTAGTATTATAAAAATCC
52286706 TAAAA-ATTTA-TATTATAAAAAT
1 TAAAATATTTAGTATTATAAAAAT
52286728 AATTTGTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 5 0.25
26 5 0.25
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAAATATTTAGTATTATAAAAATCC
Found at i:52287022 original size:18 final size:19
Alignment explanation
Indices: 52286999--52287039 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
52286989 TAAAACCTTG
52286999 TTTTTTAAAGGTTATA-TA
1 TTTTTTAAAGGTTATATTA
**
52287017 TTTTTTAAATTTTATATTA
1 TTTTTTAAAGGTTATATTA
52287036 TTTT
1 TTTT
52287040 GACTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTTTAAAGGTTATATTA
Found at i:52289485 original size:34 final size:33
Alignment explanation
Indices: 52289447--52289553 Score: 118
Period size: 34 Copynumber: 3.3 Consensus size: 33
52289437 ACATTTCATA
52289447 ATAAGATTACCGAATTATAAGATTATAGTGGAAT
1 ATAAGATTACCGAA-TATAAGATTATAGTGGAAT
*
52289481 ATAAGATTATCTC-AATGTAAGATTCAT-GT-G---
1 ATAAGATTA-C-CGAATATAAGATT-ATAGTGGAAT
52289511 ATAAGATTACCGAAATATAAGATTATAGTGGAAT
1 ATAAGATTACCG-AATATAAGATTATAGTGGAAT
52289545 ATAAGATTA
1 ATAAGATTA
52289554 TCTCAATGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
28 1 0.02
29 3 0.05
30 21 0.34
31 1 0.02
33 1 0.02
34 28 0.46
35 5 0.08
36 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.33
Consensus pattern (33 bp):
ATAAGATTACCGAATATAAGATTATAGTGGAAT
Found at i:52289535 original size:64 final size:64
Alignment explanation
Indices: 52289447--52289574 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
52289437 ACATTTCATA
*
52289447 ATAAGATTACCGAATTATAAGATTATAGTGGAATATAAGATTATCTCAATGTAAGATTCATGTG
1 ATAAGATTACCGAAATATAAGATTATAGTGGAATATAAGATTATCTCAATGTAAGATTCATGTG
52289511 ATAAGATTACCGAAATATAAGATTATAGTGGAATATAAGATTATCTCAATGTAAGATTCATGTG
1 ATAAGATTACCGAAATATAAGATTATAGTGGAATATAAGATTATCTCAATGTAAGATTCATGTG
52289575 TTTTGTTGAC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (64 bp):
ATAAGATTACCGAAATATAAGATTATAGTGGAATATAAGATTATCTCAATGTAAGATTCATGTG
Found at i:52289566 original size:34 final size:34
Alignment explanation
Indices: 52289464--52289568 Score: 130
Period size: 34 Copynumber: 3.2 Consensus size: 34
52289454 TACCGAATTA
52289464 TAAGATTATAGTGGAATATAAGATTATCTCAATG
1 TAAGATTATAGTGGAATATAAGATTATCTCAATG
* ** *
52289498 TAAGATTCAT-GT-G---ATAAGATTACCGAAATA
1 TAAGATT-ATAGTGGAATATAAGATTATCTCAATG
52289528 TAAGATTATAGTGGAATATAAGATTATCTCAATG
1 TAAGATTATAGTGGAATATAAGATTATCTCAATG
52289562 TAAGATT
1 TAAGATT
52289569 CATGTGTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
29 2 0.04
30 22 0.39
31 1 0.02
33 1 0.02
34 29 0.51
35 2 0.04
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (34 bp):
TAAGATTATAGTGGAATATAAGATTATCTCAATG
Found at i:52294304 original size:32 final size:32
Alignment explanation
Indices: 52294268--52294333 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
52294258 TTTAGTGTAG
52294268 ATATGGCCTTAAGGTGAATCAATGGGTCACTC
1 ATATGGCCTTAAGGTGAATCAATGGGTCACTC
52294300 ATATGGCCTTAAGGTGAATCAATGGGTCACTC
1 ATATGGCCTTAAGGTGAATCAATGGGTCACTC
52294332 AT
1 AT
52294334 TTTGTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (32 bp):
ATATGGCCTTAAGGTGAATCAATGGGTCACTC
Found at i:52302217 original size:63 final size:63
Alignment explanation
Indices: 52302124--52302244 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
52302114 CCTTCACGAG
* * * * *
52302124 AAGCGGTCCGGTACTCAAATCCTTAGCTTTGGCTTCAGTATGCTCAGGTTCTTCCTCCGCAAC
1 AAGCGGTCCGGTACTCAAATCCTCACCTTTGGCTTCAGTAGGATCAGGTACTTCCTCCGCAAC
*
52302187 AAGCGGTCTGGTACTCAAATCCTCACCTTTGGCTTCAGTAGGATCAGGTACTTCCTCC
1 AAGCGGTCCGGTACTCAAATCCTCACCTTTGGCTTCAGTAGGATCAGGTACTTCCTCC
52302245 ATGGGAAGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.30
Consensus pattern (63 bp):
AAGCGGTCCGGTACTCAAATCCTCACCTTTGGCTTCAGTAGGATCAGGTACTTCCTCCGCAAC
Found at i:52304907 original size:7 final size:7
Alignment explanation
Indices: 52304895--52304929 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
52304885 GGGGTTAGTA
52304895 CGAGCCC
1 CGAGCCC
52304902 CGAGCCC
1 CGAGCCC
52304909 CGAGCCC
1 CGAGCCC
52304916 CGAGCCC
1 CGAGCCC
52304923 CGAGCCC
1 CGAGCCC
52304930 TTAAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.57, G:0.29, T:0.00
Consensus pattern (7 bp):
CGAGCCC
Found at i:52307569 original size:24 final size:24
Alignment explanation
Indices: 52307542--52307592 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
52307532 TCTTGAGCAA
52307542 TTTAA-TTT-TTTTCTTTTATGTTTT
1 TTTAACTTTCTTTT-TTTTAT-TTTT
*
52307566 TTTAACTTTCTTTTTTTTCTTTTT
1 TTTAACTTTCTTTTTTTTATTTTT
52307590 TTT
1 TTT
52307593 CCATTCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 12 0.50
25 8 0.33
26 4 0.17
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTAACTTTCTTTTTTTTATTTTT
Found at i:52309768 original size:22 final size:22
Alignment explanation
Indices: 52309719--52309762 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
52309709 TTTTTTCAAG
*
52309719 AATATTTATATTATTTTAATTT
1 AATATTTATAATATTTTAATTT
*
52309741 AATATTTTTAATATTTT-ATTT
1 AATATTTATAATATTTTAATTT
52309762 A
1 A
52309763 TTTATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATATTTATAATATTTTAATTT
Found at i:52310511 original size:16 final size:16
Alignment explanation
Indices: 52310490--52310522 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52310480 CGACCCACCC
52310490 ATATTAATTTTT-TATA
1 ATATT-ATTTTTATATA
52310506 ATATTATTTTTATATA
1 ATATTATTTTTATATA
52310522 A
1 A
52310523 AAATAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTATTTTTATATA
Found at i:52311240 original size:25 final size:24
Alignment explanation
Indices: 52311189--52311251 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
52311179 TTTTGAGCAA
* *
52311189 TTTAATTTTTTTCTTTTATGTTTT
1 TTTAATTTCTTTCTTTTATCTTTT
52311213 TTTAACTTTCTTTCTTTT-TCTTTAT
1 TTTAA-TTTCTTTCTTTTATCTTT-T
52311238 TTTCAATTCTCTTT
1 TTT-AATT-TCTTT
52311252 TGCTTCTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 9 0.27
25 17 0.52
26 7 0.21
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTAATTTCTTTCTTTTATCTTTT
Found at i:52312459 original size:23 final size:23
Alignment explanation
Indices: 52312433--52312481 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
52312423 ACGAGATTTC
52312433 TTAAAAA-TATATAAATA-ATTACA
1 TTAAAAATTA-ATAAA-ACATTACA
*
52312456 TTAATAATTAATAAAACATTACA
1 TTAAAAATTAATAAAACATTACA
52312479 TTA
1 TTA
52312482 CCATTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 1 0.04
23 20 0.87
24 2 0.09
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAAATTAATAAAACATTACA
Found at i:52315649 original size:22 final size:24
Alignment explanation
Indices: 52315624--52315668 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
52315614 CGTGACAATT
52315624 AATTAGTTTTTA-A-AATTTTTAA
1 AATTAGTTTTTATATAATTTTTAA
*
52315646 AATTATTTTTTATATAATTTTTA
1 AATTAGTTTTTATATAATTTTTA
52315669 TACTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
AATTAGTTTTTATATAATTTTTAA
Found at i:52315676 original size:33 final size:32
Alignment explanation
Indices: 52315630--52315691 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
52315620 AATTAATTAG
*
52315630 TTTTTAAAATTTTTAAAATTATTTTTTATATAA
1 TTTTTAAAATTTTTAAAA-TACTTTTTATATAA
* *
52315663 TTTTTATACTTTTTAAAATACTTTTTATA
1 TTTTTAAAATTTTTAAAATACTTTTTATA
52315692 ATTGATGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTTAAAATTTTTAAAATACTTTTTATATAA
Found at i:52322605 original size:17 final size:16
Alignment explanation
Indices: 52322583--52322630 Score: 66
Period size: 13 Copynumber: 3.1 Consensus size: 16
52322573 ATAATTTTAA
52322583 AATATAATTTAAAATTG
1 AATATAATTT-AAATTG
52322600 AATATAATTT-AA-T-
1 AATATAATTTAAATTG
52322613 AATATAATTTAAATTG
1 AATATAATTTAAATTG
52322629 AA
1 AA
52322631 CGATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 10 0.36
14 3 0.11
15 3 0.11
16 2 0.07
17 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
AATATAATTTAAATTG
Found at i:52322637 original size:30 final size:29
Alignment explanation
Indices: 52322571--52322637 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 29
52322561 ATGAACCGAT
52322571 AGATAATTTTAAAATATAATTTAAAATTGA
1 AGATAA-TTTAAAATATAATTTAAAATTGA
*
52322601 ATATAATTTAATAATATAATTT-AAATTGA
1 AGATAATTTAA-AATATAATTTAAAATTGA
52322630 ACGATAAT
1 A-GATAAT
52322638 AATTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (29 bp):
AGATAATTTAAAATATAATTTAAAATTGA
Found at i:52326026 original size:15 final size:16
Alignment explanation
Indices: 52326006--52326036 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52325996 ACATGTTTAA
52326006 TATTTTT-ATATAATT
1 TATTTTTAATATAATT
52326021 TATTTTTAATATAATT
1 TATTTTTAATATAATT
52326037 ATTATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAATATAATT
Found at i:52348240 original size:14 final size:13
Alignment explanation
Indices: 52348206--52348253 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
52348196 ATCAATAAAA
52348206 TTTATTGAAAATT
1 TTTATTGAAAATT
*
52348219 TTTGTTGAAAATT
1 TTTATTGAAAATT
52348232 TTTATTTG-AAA--
1 TTTA-TTGAAAATT
52348243 TTTATTGAAAA
1 TTTATTGAAAA
52348254 AAATAACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 18 0.58
14 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (13 bp):
TTTATTGAAAATT
Found at i:52349185 original size:23 final size:23
Alignment explanation
Indices: 52349159--52349214 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
52349149 CTTGTATCAG
52349159 TTTAGTTTAAATTCATTTTATCT
1 TTTAGTTTAAATTCATTTTATCT
*
52349182 TTTAGTTTAAATTTATTTTATCT
1 TTTAGTTTAAATTCATTTTATCT
52349205 TTATA-TTTAA
1 TT-TAGTTTAA
52349215 TTTTTTGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 29 0.94
24 2 0.06
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTAGTTTAAATTCATTTTATCT
Found at i:52352519 original size:9 final size:9
Alignment explanation
Indices: 52352505--52352541 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52352495 TATAGTTTGA
52352505 TATTCGAAT
1 TATTCGAAT
52352514 TATTCGAAT
1 TATTCGAAT
*
52352523 TATTCGAGT
1 TATTCGAAT
52352532 TATTCGAAT
1 TATTCGAAT
52352541 T
1 T
52352542 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:52352612 original size:9 final size:9
Alignment explanation
Indices: 52352595--52352625 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52352585 TCGAGTTGAT
52352595 TCGAATAAC
1 TCGAATAAC
*
52352604 TCGATTAAC
1 TCGAATAAC
52352613 TCGAATAAC
1 TCGAATAAC
52352622 TCGA
1 TCGA
52352626 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:52364450 original size:5 final size:5
Alignment explanation
Indices: 52364437--52364469 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
52364427 AACATTAACC
*
52364437 TATAC TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
52364470 GCTTCCTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:52365490 original size:27 final size:23
Alignment explanation
Indices: 52365438--52365483 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
52365428 AACTTTAACA
52365438 TTACCTTGTTTAGAAGGACTGAT
1 TTACCTTGTTTAGAAGGACTGAT
52365461 TTACCTTGTTTAGAAGGACTGAT
1 TTACCTTGTTTAGAAGGACTGAT
52365484 GGTTTTATTT
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:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (23 bp):
TTACCTTGTTTAGAAGGACTGAT
Found at i:52368662 original size:10 final size:10
Alignment explanation
Indices: 52368648--52368681 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
52368638 AGGTATGGTT
*
52368648 TGTATTGTAT
1 TGTATTGTAG
52368658 TGTATTGTAG
1 TGTATTGTAG
*
52368668 TCTATTGTAG
1 TGTATTGTAG
52368678 TGTA
1 TGTA
52368682 ATCTATACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.03, G:0.24, T:0.53
Consensus pattern (10 bp):
TGTATTGTAG
Found at i:52375763 original size:3 final size:3
Alignment explanation
Indices: 52375755--52375785 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
52375745 ACAATTAGAG
*
52375755 AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
52375786 AATGAATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52382371 original size:5 final size:5
Alignment explanation
Indices: 52382363--52382390 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
52382353 GAATGCGAAT
52382363 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
52382391 AATTGAAGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:52385245 original size:15 final size:16
Alignment explanation
Indices: 52385227--52385261 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
52385217 TGGGTTCCAA
52385227 AATTTGGTTTT-AAAG
1 AATTTGGTTTTCAAAG
52385242 AA-TTGGTTTTCAAAG
1 AATTTGGTTTTCAAAG
52385257 AATTT
1 AATTT
52385262 TAAACATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.44
15 8 0.44
16 2 0.11
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (16 bp):
AATTTGGTTTTCAAAG
Found at i:52385509 original size:16 final size:17
Alignment explanation
Indices: 52385490--52385527 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
52385480 AATATTAAAA
52385490 CTAATG-CATAAAACTT
1 CTAATGACATAAAACTT
*
52385506 CTAATGTAGATAAAACTT
1 CTAATG-ACATAAAACTT
52385524 CTAA
1 CTAA
52385528 GTCACAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (17 bp):
CTAATGACATAAAACTT
Found at i:52386181 original size:21 final size:21
Alignment explanation
Indices: 52386150--52386204 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
52386140 GGTGGTGTCG
* * *
52386150 AAGTATAAGAGATATGTATCG
1 AAGTATGAGAGATATATATCA
* *
52386171 GAGTATGAGAGATGTATATCA
1 AAGTATGAGAGATATATATCA
52386192 AAGTATGAGAGAT
1 AAGTATGAGAGAT
52386205 GTGTTAGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.27, T:0.27
Consensus pattern (21 bp):
AAGTATGAGAGATATATATCA
Found at i:52391950 original size:26 final size:26
Alignment explanation
Indices: 52391920--52391973 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
52391910 TCACTTTCAT
*
52391920 GTGACATCGTCAAATAGGACCATAAA
1 GTGACATCGTCAAATACGACCATAAA
52391946 GTGACATCGTCAAATACGACCATAAA
1 GTGACATCGTCAAATACGACCATAAA
52391972 GT
1 GT
52391974 CTAGGCCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (26 bp):
GTGACATCGTCAAATACGACCATAAA
Found at i:52397003 original size:5 final size:5
Alignment explanation
Indices: 52396993--52397020 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
52396983 GAAAGCGAAT
52396993 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
52397021 AATTCAAGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:52397574 original size:24 final size:23
Alignment explanation
Indices: 52397529--52397575 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
52397519 AAGCAATACT
*
52397529 ACATGCATAAGTAAGACTAAAAA
1 ACATGCATAAGAAAGACTAAAAA
52397552 ACATGCCATAAGAAGAGAC-AAAAA
1 ACATG-CATAAGAA-AGACTAAAAA
52397576 CATCTAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (23 bp):
ACATGCATAAGAAAGACTAAAAA
Found at i:52397987 original size:21 final size:21
Alignment explanation
Indices: 52397927--52397989 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
52397917 TTCTTCTCTG
* *
52397927 CTCTGCTTCCCTCACTGCAGC
1 CTCTGCTTCCCTCGCTGCTGC
* * *
52397948 CTCTGCTGCTCTCGTTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
52397969 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
52397990 ATCAACTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.03, C:0.44, G:0.19, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTGC
Found at i:52398063 original size:86 final size:87
Alignment explanation
Indices: 52397947--52398149 Score: 300
Period size: 86 Copynumber: 2.3 Consensus size: 87
52397937 CTCACTGCAG
* * * * * *
52397947 CCTCTGCTGCTCTCGTTGCTGCCTCTGCTTCCCTCGCTGCTGCATCAACTTTAAGTTGTAGCTGG
1 CCTCAGCTTCTCTCGATGCTGCCTCTGCTTCCCTCACCGCTGCATCAACTCTAAGTTGTAGCTGG
*
52398012 AGTTCTTTATATTTTCTTTGAA
66 AGTTCTTCATATTTTCTTTGAA
***
52398034 CCTCAGCTTCTCTC-ATGCTGCCTCTGCTTCCCTCACCGCTGCATTTGCTCTAAGTTGTAGCTGG
1 CCTCAGCTTCTCTCGATGCTGCCTCTGCTTCCCTCACCGCTGCATCAACTCTAAGTTGTAGCTGG
52398098 AGTTCTTCATATTTTCTTTGAA
66 AGTTCTTCATATTTTCTTTGAA
*
52398120 CCTTAGCTTCTCTCGATGCTGCCTCTGCTT
1 CCTCAGCTTCTCTCGATGCTGCCTCTGCTT
52398150 TAAGTTGAGT
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 77 0.74
87 27 0.26
ACGTcount: A:0.12, C:0.30, G:0.17, T:0.40
Consensus pattern (87 bp):
CCTCAGCTTCTCTCGATGCTGCCTCTGCTTCCCTCACCGCTGCATCAACTCTAAGTTGTAGCTGG
AGTTCTTCATATTTTCTTTGAA
Found at i:52399905 original size:41 final size:40
Alignment explanation
Indices: 52399860--52399987 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 40
52399850 ATGTTTTTTT
*
52399860 GCGGCACTTTCACAAAAACGCAGCTAAAACCCTGAGCTTTA
1 GCGGCACTTTCA-AAAAACGCAGCTAAAACCCTGAGCATTA
* * * * * *
52399901 GCGGCGCCTTTCTAAAAATGCCGCTAAAACCCCGAACATTA
1 GCGGC-ACTTTCAAAAAACGCAGCTAAAACCCTGAGCATTA
* * *
52399942 GCGGCGCTTAAT-AAAAAACGCTGCTAAAACCCTGAGCATTG
1 GCGGCACTT--TCAAAAAACGCAGCTAAAACCCTGAGCATTA
52399983 GCGGC
1 GCGGC
52399988 GCTATTTTAA
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
40 3 0.04
41 61 0.87
42 6 0.09
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (40 bp):
GCGGCACTTTCAAAAAACGCAGCTAAAACCCTGAGCATTA
Found at i:52399999 original size:82 final size:82
Alignment explanation
Indices: 52399873--52400031 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 82
52399863 GCACTTTCAC
*
52399873 AAAAACGCAGCTAAAACCCTGAGCTTTAGCGGCGCCTTTCTAAAAATGCCGCTAAAACCC-CGAA
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCCTTTCTAAAAATGCCGCTAAAACCCAC-AA
52399937 CATTAGCGGCGCTTAATA
65 CATTAGCGGCGCTTAATA
* * * **
52399955 AAAAACGCTGCTAAAACCCTGAGCATTGGCGGCG-CTATTTTAAAAATGCCTTTAAAACCCACAA
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCCT-TTCTAAAAATGCCGCTAAAACCCACAA
52400019 CATTAGCGGCGCT
65 CATTAGCGGCGCT
52400032 ACTCCAGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 2 0.03
82 66 0.96
83 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (82 bp):
AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCCTTTCTAAAAATGCCGCTAAAACCCACAAC
ATTAGCGGCGCTTAATA
Found at i:52400000 original size:41 final size:40
Alignment explanation
Indices: 52399873--52400000 Score: 139
Period size: 41 Copynumber: 3.1 Consensus size: 40
52399863 GCACTTTCAC
* *
52399873 AAAAACGCAGCTAAAACCCTGAGCTTTAGCGGCGCCTTTCT
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCG-CTTTTT
* * * * * *
52399914 AAAAATGCCGCTAAAACCCCGAACATTAGCGGCGCTTAATA
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCTT-TTT
* *
52399955 AAAAACGCTGCTAAAACCCTGAGCATTGGCGGCGCTATTTT
1 AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCT-TTTT
52399996 AAAAA
1 AAAAA
52400001 TGCCTTTAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
40 3 0.04
41 66 0.94
42 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (40 bp):
AAAAACGCAGCTAAAACCCTGAGCATTAGCGGCGCTTTTT
Found at i:52400011 original size:41 final size:40
Alignment explanation
Indices: 52399883--52400031 Score: 138
Period size: 41 Copynumber: 3.6 Consensus size: 40
52399873 AAAAACGCAG
* * * *
52399883 CTAAAACCCTGAGCTTTAGCGGCGCCTTTCTAAAAATGCCG
1 CTAAAACCCTGAACATTAGCGGCG-CTTTATAAAAATGCCT
* * *
52399924 CTAAAACCCCGAACATTAGCGGCGCTTAATAAAAA-ACGCT
1 CTAAAACCCTGAACATTAGCGGCGCTTTATAAAAATGC-CT
* * *
52399964 GCTAAAACCCTGAGCATTGGCGGCGCTATTTTAAAAATGCCT
1 -CTAAAACCCTGAACATTAGCGGCGCT-TTATAAAAATGCCT
* **
52400006 TTAAAACCCACAACATTAGCGGCGCT
1 CTAAAACCCTGAACATTAGCGGCGCT
52400032 ACTCCAGAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
39 1 0.01
40 10 0.12
41 65 0.76
42 9 0.10
43 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (40 bp):
CTAAAACCCTGAACATTAGCGGCGCTTTATAAAAATGCCT
Found at i:52400331 original size:37 final size:37
Alignment explanation
Indices: 52400287--52400361 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
52400277 AGTTAGGGGG
52400287 TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
1 TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
*
52400324 TTTAGAAGATGATGAACAGGATGCAAAAAGTGGGGTT
1 TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
52400361 T
1 T
52400362 CTTATTATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.04, G:0.32, T:0.25
Consensus pattern (37 bp):
TTTAGAAGATGATGAAAAGGATGCAAAAAGTGGGGTT
Found at i:52405709 original size:21 final size:21
Alignment explanation
Indices: 52405679--52405718 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52405669 CCTCAATGCA
* *
52405679 ATTGGGTCATTGCGAGATGAC
1 ATTGGCTCATTACGAGATGAC
52405700 ATTGGCTCATTACGAGATG
1 ATTGGCTCATTACGAGATG
52405719 TAGTTAGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (21 bp):
ATTGGCTCATTACGAGATGAC
Found at i:52410106 original size:26 final size:26
Alignment explanation
Indices: 52409964--52410115 Score: 71
Period size: 26 Copynumber: 5.9 Consensus size: 26
52409954 AAACAATTTT
* * *
52409964 AAACAATTTAAAATAAACATTACATG
1 AAACAATTTAAAATAAATAATATATG
* * * * * **
52409990 AAATAGTTTAAAAGAAATGACACGT-
1 AAACAATTTAAAATAAATAATATATG
* *
52410015 AAA-AATCTAAAATAAATAATATACATA
1 AAACAATTTAAAATAAATAATAT--ATG
* *
52410042 AAACAGTTTAAGAT-AA-AATA-ATAG
1 AAACAATTTAAAATAAATAATATAT-G
**
52410066 AAAGCAATTCGAAATAAATAATATATG
1 AAA-CAATTTAAAATAAATAATATATG
**
52410093 AAACAATTTAAAATTGATAATAT
1 AAACAATTTAAAATAAATAATAT
52410116 CAAACAGTTT
Statistics
Matches: 90, Mismatches: 27, Indels: 18
0.67 0.20 0.13
Matches are distributed among these distances:
23 2 0.02
24 16 0.18
25 10 0.11
26 40 0.44
27 13 0.14
28 9 0.10
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (26 bp):
AAACAATTTAAAATAAATAATATATG
Found at i:52410157 original size:14 final size:14
Alignment explanation
Indices: 52410138--52410168 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52410128 TATGAACAAT
52410138 ATAAATAAAATGAA
1 ATAAATAAAATGAA
*
52410152 ATAAATAAAATGTA
1 ATAAATAAAATGAA
52410166 ATA
1 ATA
52410169 TGTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (14 bp):
ATAAATAAAATGAA
Found at i:52410213 original size:26 final size:26
Alignment explanation
Indices: 52410178--52410227 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
52410168 ATGTTTAAAA
52410178 AATAATAATAATGAATATAA-AAATTCG
1 AATAATAATAAT-AA-ATAACAAATTCG
52410205 AATAA-AATAATAAATAACAAATT
1 AATAATAATAATAAATAACAAATT
52410228 AAAGGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.18
25 7 0.32
26 6 0.27
27 5 0.23
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (26 bp):
AATAATAATAATAAATAACAAATTCG
Found at i:52410972 original size:15 final size:16
Alignment explanation
Indices: 52410952--52410982 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52410942 ATTATTTAGT
52410952 ATAAAAG-GAAAAAAA
1 ATAAAAGAGAAAAAAA
52410967 ATAAAAGAGAAAAAAA
1 ATAAAAGAGAAAAAAA
52410983 TCGAACAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (16 bp):
ATAAAAGAGAAAAAAA
Found at i:52433648 original size:69 final size:69
Alignment explanation
Indices: 52433538--52433974 Score: 331
Period size: 69 Copynumber: 6.6 Consensus size: 69
52433528 AGCTTACACT
* * *
52433538 CAAAATAGCTCGCGGACCTACG--CTCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCGCAG
1 CAAAACAGCTCGCGAACCTACGTTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCGCAG
*
52433601 CCTT
66 CCTC
* * * * *
52433605 CAAAACAGCTCGTGAACCTACATTCCCAACTGATATTATAAAGGCTCACCAGTTTAAGATCACAG
1 CAAAACAGCTCGCGAACCTACGTTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCGCAG
52433670 CCTC
66 CCTC
* * * * * * * * *
52433674 CAAAACAGTTCACGGACCTATGCTCCCAGCTAATATTATAAAGGCTCGCTGGTTTAAGATCGCAA
1 CAAAACAGCTCGCGAACCTACGTTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCGCAG
52433739 CCTC
66 CCTC
** * *
52433743 C-AAA-A-----C-AA-C-AC--TCCCAGTTGATATTATAAAGACTCGCCGGTCTAAGATCGCAG
1 CAAAACAGCTCGCGAACCTACGTTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCGCAG
52433796 CCTC
66 CCTC
* * * *
52433800 CAAAATAGCTCGCGGACCTACGTTCCCAATTGATATTATAAAGGCTCGCTGGTTT---A----AG
1 CAAAACAGCTCGCGAACCTACGTTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCGCAG
52433858 CCTC
66 CCTC
* * * * * * * ** * *
52433862 AAAAACAGCTCACGGACCTAAGTTCCTAGCTAATATTATAAAGGCTAACCGGTTTAAGATCGTAA
1 CAAAACAGCTCGCGAACCTACGTTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCGCAG
52433927 CCTC
66 CCTC
* * * * ** *
52433931 TAAAGCAGCTCGCAAACCTGCGTTCTTAGCTGATATTATAAAGG
1 CAAAACAGCTCGCGAACCTACGTTCCCAACTGATATTATAAAGG
52433975 TTAGTTGATT
Statistics
Matches: 292, Mismatches: 57, Indels: 40
0.75 0.15 0.10
Matches are distributed among these distances:
57 41 0.14
58 3 0.01
59 2 0.01
60 1 0.00
61 1 0.00
62 51 0.17
64 1 0.00
65 2 0.01
66 2 0.01
67 21 0.07
68 3 0.01
69 164 0.56
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (69 bp):
CAAAACAGCTCGCGAACCTACGTTCCCAACTGATATTATAAAGGCTCGCCGGTTTAAGATCGCAG
CCTC
Found at i:52433789 original size:57 final size:57
Alignment explanation
Indices: 52433696--52433804 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
52433686 CGGACCTATG
* * *
52433696 CTCCCAGCTAATATTATAAAGGCTCGCTGGTTTAAGATCGCAACCTCCAAAACAACA
1 CTCCCAGCTAATATTATAAAGACTCGCCGGTCTAAGATCGCAACCTCCAAAACAACA
* * *
52433753 CTCCCAGTTGATATTATAAAGACTCGCCGGTCTAAGATCGCAGCCTCCAAAA
1 CTCCCAGCTAATATTATAAAGACTCGCCGGTCTAAGATCGCAACCTCCAAAA
52433805 TAGCTCGCGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (57 bp):
CTCCCAGCTAATATTATAAAGACTCGCCGGTCTAAGATCGCAACCTCCAAAACAACA
Found at i:52433916 original size:62 final size:62
Alignment explanation
Indices: 52433794--52433919 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 62
52433784 CTAAGATCGC
* * * * * * ** *
52433794 AGCCTCCAAAATAGCTCGCGGACCTACGTTCCCAATTGATATTATAAAGGCTCGCTGGTTTA
1 AGCCTCAAAAACAGCTCACGGACCTAAGTTCCCAACTAATATTATAAAGGCTAACCGGTTTA
* *
52433856 AGCCTCAAAAACAGCTCACGGACCTAAGTTCCTAGCTAATATTATAAAGGCTAACCGGTTTA
1 AGCCTCAAAAACAGCTCACGGACCTAAGTTCCCAACTAATATTATAAAGGCTAACCGGTTTA
52433918 AG
1 AG
52433920 ATCGTAACCT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (62 bp):
AGCCTCAAAAACAGCTCACGGACCTAAGTTCCCAACTAATATTATAAAGGCTAACCGGTTTA
Found at i:52436273 original size:22 final size:22
Alignment explanation
Indices: 52436231--52436275 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
52436221 TATAATAAGA
**
52436231 TTTTAATTTAACATGCTTAATT
1 TTTTAATTTAACATGAATAATT
*
52436253 TTTTAATTTAACTTGAATAATT
1 TTTTAATTTAACATGAATAATT
52436275 T
1 T
52436276 CACTCGATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACATGAATAATT
Found at i:52437608 original size:23 final size:20
Alignment explanation
Indices: 52437561--52437597 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
52437551 CAGTTAGTTT
*
52437561 TATGAGGTGGAATTAATTAA
1 TATGACGTGGAATTAATTAA
52437581 -ATGACGTGGAATTAATT
1 TATGACGTGGAATTAATT
52437598 TAAGATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (20 bp):
TATGACGTGGAATTAATTAA
Found at i:52440318 original size:31 final size:32
Alignment explanation
Indices: 52440283--52440352 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
52440273 ACTTTTTTTA
* *
52440283 AATTAAATTTAGCTCTTAATCTTTT-AAAAAG
1 AATTAAATTTAACTATTAATCTTTTGAAAAAG
*
52440314 AATTAAATTTAATTATTAATCTTTTGAAAAAG
1 AATTAAATTTAACTATTAATCTTTTGAAAAAG
*
52440346 AGTTAAA
1 AATTAAA
52440353 ATATTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.65
32 12 0.35
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (32 bp):
AATTAAATTTAACTATTAATCTTTTGAAAAAG
Found at i:52440878 original size:22 final size:21
Alignment explanation
Indices: 52440853--52440903 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
52440843 TGTTGGCAAA
52440853 TTTATAAAATATTTAAAAATAT
1 TTTATAAAATATTTAAAAAT-T
* * *
52440875 TTTATATTAATATTTATATATT
1 TTTATA-AAATATTTAAAAATT
52440897 TTTATAA
1 TTTATAA
52440904 TAAATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATAAAATATTTAAAAATT
Found at i:52442554 original size:13 final size:14
Alignment explanation
Indices: 52442531--52442574 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
52442521 TTTTAGATTA
52442531 AAATATTATTTTTT
1 AAATATTATTTTTT
52442545 AAAT-TTATTTTTATT
1 AAATATTA-TTTT-TT
52442560 GAAATATTATTTTTT
1 -AAATATTATTTTTT
52442575 TTATAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 4 0.15
16 8 0.31
17 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
AAATATTATTTTTT
Found at i:52448786 original size:18 final size:19
Alignment explanation
Indices: 52448763--52448803 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
52448753 AGCACCACCT
*
52448763 ATAAAAAATAAA-AATTTA
1 ATAAAAAATAAATAAATTA
52448781 AT-AAAAATAAATAAATTA
1 ATAAAAAATAAATAAATTA
52448799 ATAAA
1 ATAAA
52448804 TTAAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 9 0.45
18 9 0.45
19 2 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAAAATAAATAAATTA
Found at i:52448788 original size:17 final size:18
Alignment explanation
Indices: 52448766--52448803 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
52448756 ACCACCTATA
*
52448766 AAAAATAAA-AATTTAAT
1 AAAAATAAATAAATTAAT
52448783 AAAAATAAATAAATTAAT
1 AAAAATAAATAAATTAAT
52448801 AAA
1 AAA
52448804 TTAAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAAATAAATTAAT
Found at i:52451449 original size:69 final size:69
Alignment explanation
Indices: 52451361--52451768 Score: 343
Period size: 69 Copynumber: 6.2 Consensus size: 69
52451351 CTTGCAACTT
* *
52451361 CAAAATAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCAGTTTAAGATCCCAG
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCAGTTTAAGATCGCAG
*
52451426 CCTT
66 CCTC
* * * ** * *
52451430 CAAGACAGCTCTCGAACCTACATTCCCAACTGATATTATAAAGGCTCACCAGTTTAAGATCGTAG
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCAGTTTAAGATCGCAG
52451495 CCTC
66 CCTC
* * * * ** *
52451499 CAAAACAACTCACGGACCTACGCTCCCAGCTAATATTATAAAGGCTCGCTGGTTTAAGATCGCAA
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCAGTTTAAGATCGCAG
52451564 CCTC
66 CCTC
** * *
52451568 CAAAACA--------A-C-A--CTCCCAGTTGATATTATAAAGACTCGCC-GATCTAAGATCGCA
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCAG-TTTAAGATCGCA
52451620 GCCTC
65 GCCTC
* * ***
52451625 CAAAACAGCTCGCGGACCTACGTTCCCAATTGATATTATAAAGGCTCGTTGGTTT-A-A--G--G
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCAGTTTAAGATCGCAG
52451684 -CTC
66 CCTC
* * * * ** * * *
52451687 CAAAACAGCTCACGGACCTACGTTCCCAGCTAATATTATAAAGGCTAACCGGTTTAAGATCGTAA
1 CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCAGTTTAAGATCGCAG
52451752 CCTC
66 CCTC
*
52451756 CAAAGCAGCTCGC
1 CAAAACAGCTCGC
52451769 AAACCTGCGT
Statistics
Matches: 272, Mismatches: 46, Indels: 42
0.76 0.13 0.12
Matches are distributed among these distances:
56 1 0.00
57 46 0.17
59 1 0.00
60 1 0.00
61 1 0.00
62 50 0.18
63 2 0.01
64 1 0.00
65 2 0.01
66 2 0.01
67 2 0.01
68 1 0.00
69 161 0.59
70 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (69 bp):
CAAAACAGCTCGCGGACCTACGCTCCCAACTGATATTATAAAGGCTCGCCAGTTTAAGATCGCAG
CCTC
Found at i:52451614 original size:57 final size:57
Alignment explanation
Indices: 52451521--52451631 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
52451511 CGGACCTACG
* * * *
52451521 CTCCCAGCTAATATTATAAAGGCTCGCTGGTTTAAGATCGCAACCTCCAAAACAACA
1 CTCCCAGCTAATATTATAAAGACTCGCCGATCTAAGATCGCAACCTCCAAAACAACA
* * *
52451578 CTCCCAGTTGATATTATAAAGACTCGCCGATCTAAGATCGCAGCCTCCAAAACA
1 CTCCCAGCTAATATTATAAAGACTCGCCGATCTAAGATCGCAACCTCCAAAACA
52451632 GCTCGCGGAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (57 bp):
CTCCCAGCTAATATTATAAAGACTCGCCGATCTAAGATCGCAACCTCCAAAACAACA
Found at i:52451741 original size:62 final size:62
Alignment explanation
Indices: 52451622--52451744 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 62
52451612 AGATCGCAGC
* * * ****
52451622 CTCCAAAACAGCTCGCGGACCTACGTTCCCAATTGATATTATAAAGGCTCGTTGGTTTAAGG
1 CTCCAAAACAGCTCACGGACCTACGTTCCCAACTAATATTATAAAGGCTAACCGGTTTAAGG
*
52451684 CTCCAAAACAGCTCACGGACCTACGTTCCCAGCTAATATTATAAAGGCTAACCGGTTTAAG
1 CTCCAAAACAGCTCACGGACCTACGTTCCCAACTAATATTATAAAGGCTAACCGGTTTAAG
52451745 ATCGTAACCT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (62 bp):
CTCCAAAACAGCTCACGGACCTACGTTCCCAACTAATATTATAAAGGCTAACCGGTTTAAGG
Found at i:52452840 original size:17 final size:18
Alignment explanation
Indices: 52452818--52452855 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
52452808 TTTTAAAATA
52452818 TTTAAAAATATTTTT-AT
1 TTTAAAAATATTTTTAAT
* *
52452835 TTTAAATATTTTTTTAAT
1 TTTAAAAATATTTTTAAT
52452853 TTT
1 TTT
52452856 CTAAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAAAAATATTTTTAAT
Found at i:52455150 original size:4 final size:4
Alignment explanation
Indices: 52455141--52455212 Score: 68
Period size: 4 Copynumber: 19.5 Consensus size: 4
52455131 ATCGGGGAGG
* *
52455141 AAGA AAGA AAGG AAGA AAGA AA-A AAAA AAGA AA-A AGAGA AAGA AAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA
52455187 AAGA AAG- AAG- AAG- AAG- AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
52455213 AAGAAGAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
3 20 0.33
4 38 0.63
5 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:52455174 original size:6 final size:6
Alignment explanation
Indices: 52455156--52455243 Score: 74
Period size: 6 Copynumber: 14.5 Consensus size: 6
52455146 AGAAAGGAAG
* *
52455156 AAAGAA AAA-AA AAAGAA AAAGAG AAAGAA AGAAGAA AGAAGAA GAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA A-AAGAA AAAGAA
* * *
52455205 GAAAGAA AAAGAA GAA-AA AAATAA AATA-AA AAATAA AAA
1 -AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAA
52455244 AATTTCAACA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
5 10 0.14
6 42 0.60
7 18 0.26
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:52455180 original size:23 final size:23
Alignment explanation
Indices: 52455154--52455223 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
52455144 AAAGAAAGGA
52455154 AGAAAGAAAAAAAAAAGAAAAAG
1 AGAAAGAAAAAAAAAAGAAAAAG
* * *
52455177 AGAAAGAAAGAAGAAAGAAGAAG
1 AGAAAGAAAAAAAAAAGAAAAAG
52455200 A-AGAAGAAAGAAAAAGAAGAAAAA
1 AGA-AAGAAA-AAAAA-AAGAAAAA
52455224 AATAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 27 0.71
24 3 0.08
25 7 0.18
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (23 bp):
AGAAAGAAAAAAAAAAGAAAAAG
Found at i:52455216 original size:16 final size:16
Alignment explanation
Indices: 52455140--52455220 Score: 89
Period size: 16 Copynumber: 5.2 Consensus size: 16
52455130 GATCGGGGAG
*
52455140 GAAGAAAG-AAAGGAA
1 GAAGAAAGAAAAAGAA
52455155 GAAAGAAA-AAAAA-AA
1 G-AAGAAAGAAAAAGAA
*
52455170 GAA-AAAGAGAAAGAAA
1 GAAGAAAGAAAAAG-AA
*
52455186 GAAGAAAGAAGAAGAA
1 GAAGAAAGAAAAAGAA
52455202 GAAGAAAGAAAAAGAA
1 GAAGAAAGAAAAAGAA
52455218 GAA
1 GAA
52455221 AAAAATAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
13 3 0.05
14 6 0.11
15 4 0.07
16 34 0.62
17 8 0.15
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
GAAGAAAGAAAAAGAA
Found at i:52455230 original size:16 final size:16
Alignment explanation
Indices: 52455152--52455230 Score: 65
Period size: 16 Copynumber: 4.8 Consensus size: 16
52455142 AGAAAGAAAG
52455152 GAAGAAAGAAAAAA-AA
1 GAAGAAA-AAAAAAGAA
52455168 -AAGAAAAAGAGAAAGAAA
1 GAAGAAAAA-A-AAAG-AA
* *
52455186 GAAGAAAGAAGAAGAA
1 GAAGAAAAAAAAAGAA
*
52455202 GAAGAAAGAAAAAGAA
1 GAAGAAAAAAAAAGAA
52455218 GAA-AAAAATAAAA
1 GAAGAAAAA-AAAA
52455231 TAAAAAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.04
15 11 0.21
16 27 0.51
17 3 0.06
18 3 0.06
19 7 0.13
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (16 bp):
GAAGAAAAAAAAAGAA
Found at i:52455401 original size:25 final size:24
Alignment explanation
Indices: 52455373--52455423 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
52455363 CAAAATAGAA
52455373 AAAGAAGCAGCAGAAAAA-AAGAAAG
1 AAAGAAGCAG-A-AAAAAGAAGAAAG
52455398 AAAGAAGCAGAAAAAAGAAGAAAG
1 AAAGAAGCAGAAAAAAGAAGAAAG
52455422 AA
1 AA
52455424 GCAGGCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.20
24 10 0.40
25 10 0.40
ACGTcount: A:0.71, C:0.06, G:0.24, T:0.00
Consensus pattern (24 bp):
AAAGAAGCAGAAAAAAGAAGAAAG
Found at i:52455418 original size:20 final size:22
Alignment explanation
Indices: 52455373--52455427 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
52455363 CAAAATAGAA
*
52455373 AAAG-AAGCAGCAGAAAAAAAG
1 AAAGAAAGAAGCAGAAAAAAAG
52455394 AAAGAAAGAAGCAG-AAAAAAG
1 AAAGAAAGAAGCAGAAAAAAAG
52455415 -AAGAAAGAAGCAG
1 AAAGAAAGAAGCAG
52455428 GCCATTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 13 0.41
21 11 0.34
22 8 0.25
ACGTcount: A:0.67, C:0.07, G:0.25, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAGCAGAAAAAAAG
Found at i:52455585 original size:12 final size:13
Alignment explanation
Indices: 52455553--52455584 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
52455543 GCAGGGCAAA
52455553 AAAAAAAGAGAAG
1 AAAAAAAGAGAAG
*
52455566 AAAAAAAGGGAAG
1 AAAAAAAGAGAAG
52455579 AAAAAA
1 AAAAAA
52455585 GAAAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAG
Found at i:52455765 original size:8 final size:7
Alignment explanation
Indices: 52455735--52455771 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
52455725 TATTTTTGTA
*
52455735 TTTATAT
1 TTTAAAT
52455742 TTTAAAT
1 TTTAAAT
52455749 TTTAAAT
1 TTTAAAT
*
52455756 TTTAAAA
1 TTTAAAT
52455763 TTTAAAT
1 TTTAAAT
52455770 TT
1 TT
52455772 AATTCAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAAAT
Found at i:52455795 original size:23 final size:24
Alignment explanation
Indices: 52455753--52455798 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
52455743 TTAAATTTTA
52455753 AATTTTAAAATTTAAATTTAATTC
1 AATTTTAAAATTTAAATTTAATTC
* *
52455777 AATTTT-AATTTTAATTTTAATT
1 AATTTTAAAATTTAAATTTAATT
52455799 TATTTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTTTAAAATTTAAATTTAATTC
Found at i:52455800 original size:11 final size:11
Alignment explanation
Indices: 52455761--52455804 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
52455751 TAAATTTTAA
*
52455761 AATTTAAATTT
1 AATTTAATTTT
*
52455772 AATTCAATTTT
1 AATTTAATTTT
52455783 AATTTTAATTTT
1 AA-TTTAATTTT
52455795 AATTT-ATTTT
1 AATTTAATTTT
52455805 GAATACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 10 0.34
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
AATTTAATTTT
Found at i:52455970 original size:18 final size:19
Alignment explanation
Indices: 52455949--52455997 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
52455939 AATCTCATGG
52455949 TTTCAAAAAATTTC-TATC
1 TTTCAAAAAATTTCGTATC
** *
52455967 TTTCAAAATTTTTCGTGTC
1 TTTCAAAAAATTTCGTATC
52455986 -TTCAAAAAATTT
1 TTTCAAAAAATTT
52455998 TTCTCGTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (19 bp):
TTTCAAAAAATTTCGTATC
Found at i:52455996 original size:20 final size:21
Alignment explanation
Indices: 52455971--52456015 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
52455961 TCTATCTTTC
52455971 AAAA-TTTT-TCGTGTCTTCAA
1 AAAATTTTTCTCGTGT-TTCAA
52455991 AAAATTTTTCTCGTGTTTCAA
1 AAAATTTTTCTCGTGTTTCAA
52456012 AAAA
1 AAAA
52456016 AAATATTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.17
21 13 0.57
22 6 0.26
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (21 bp):
AAAATTTTTCTCGTGTTTCAA
Found at i:52456175 original size:18 final size:17
Alignment explanation
Indices: 52456154--52456406 Score: 183
Period size: 17 Copynumber: 14.3 Consensus size: 17
52456144 TTTGTGTAAA
52456154 AAAAATTTCCCGTGTTTC
1 AAAAATTT-CCGTGTTTC
* * *
52456172 AAAAATTTTCTTGTTTT
1 AAAAATTTCCGTGTTTC
*
52456189 AAAAAATTCTCGTGTTTTC
1 AAAAATTTC-CGTG-TTTC
*
52456208 AAAAATTTCAGTGTTTC
1 AAAAATTTCCGTGTTTC
* *
52456225 AAAAATTCCCGTGTTTT
1 AAAAATTTCCGTGTTTC
*
52456242 AAAAATTTCTGTGTTTTC
1 AAAAATTTCCGTG-TTTC
* *
52456260 AAAAATTTTCGTATTTTC
1 AAAAATTTCCGT-GTTTC
*
52456278 AAAAAAAAATT-CGTGTTTC
1 ---AAAAATTTCCGTGTTTC
*
52456297 AAAAA-TCCACGTGTTTTC
1 AAAAATTTC-CGTG-TTTC
*
52456315 AAAAATTTCGGTGTTTC
1 AAAAATTTCCGTGTTTC
52456332 AAAAATCTT-CGTGTTTTC
1 AAAAAT-TTCCGTG-TTTC
*
52456350 AAAAA-TTCCGGTGATTC
1 AAAAATTTCC-GTGTTTC
*
52456367 -AAAATTTTCGTGTTTTC
1 AAAAATTTCCGTG-TTTC
* *
52456384 TAAAAATTTCTGTGCTTC
1 -AAAAATTTCCGTGTTTC
52456402 AAAAA
1 AAAAA
52456407 AATTTCGATT
Statistics
Matches: 186, Mismatches: 30, Indels: 39
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.01
16 14 0.08
17 74 0.40
18 60 0.32
19 27 0.15
20 3 0.02
21 7 0.04
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (17 bp):
AAAAATTTCCGTGTTTC
Found at i:52456186 original size:17 final size:17
Alignment explanation
Indices: 52456154--52456567 Score: 173
Period size: 18 Copynumber: 23.5 Consensus size: 17
52456144 TTTGTGTAAA
*
52456154 AAAAATTTCCCGTGTTTC
1 AAAAATTT-TCGTGTTTC
* *
52456172 AAAAATTTTCTTGTTTTA
1 AAAAATTTTCGTG-TTTC
*
52456190 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
52456208 AAAAA-TTTCAGTGTTTC
1 AAAAATTTTC-GTGTTTC
** *
52456225 AAAAATTCCCGTGTTTT
1 AAAAATTTTCGTGTTTC
52456242 AAAAA-TTTCTGTGTTTTC
1 AAAAATTTTC-GTG-TTTC
*
52456260 AAAAATTTTCGTATTTTC
1 AAAAATTTTCGT-GTTTC
**
52456278 AAAAAAAAATTCGTGTTTC
1 --AAAAATTTTCGTGTTTC
***
52456297 AAAAATCCACGTGTTTTC
1 AAAAATTTTCGTG-TTTC
52456315 AAAAA-TTTCGGTGTTTC
1 AAAAATTTTC-GTGTTTC
*
52456332 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
52456350 AAAAA-TTCCGGTGATTC
1 AAAAATTTTC-GTGTTTC
52456367 -AAAATTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
52456384 TAAAAA-TTTCTGTGCTTC
1 -AAAAATTTTC-GTGTTTC
* *
52456402 AAAAAAATTTCG-ATTTC
1 -AAAAATTTTCGTGTTTC
* *
52456419 ACAAA-TGTCTGTGTTTTC
1 AAAAATTTTC-GTG-TTTC
** * * *
52456437 AATGACTCTAGTGTTTC
1 AAAAATTTTCGTGTTTC
* * * *
52456454 ACAAATTGTCATGTTTTTTTT
1 AAAAATTTTC--G--TGTTTC
*** * *
52456475 TTTAATTTGCGT-TTTG
1 AAAAATTTTCGTGTTTC
*
52456491 AAAAATTCTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
52456508 AAAAATTGTCGTGTTTTAA
1 AAAAATTTTCGTG-TTT-C
52456527 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
52456544 TAAAATTTTCATG-TTC
1 AAAAATTTTCGTGTTTC
52456560 AAAAATTT
1 AAAAATTT
52456568 CGTTTTTTTT
Statistics
Matches: 296, Mismatches: 69, Indels: 64
0.69 0.16 0.15
Matches are distributed among these distances:
15 3 0.01
16 34 0.11
17 100 0.34
18 105 0.35
19 35 0.12
20 10 0.03
21 9 0.03
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:52456329 original size:35 final size:34
Alignment explanation
Indices: 52456164--52456406 Score: 215
Period size: 35 Copynumber: 6.9 Consensus size: 34
52456154 AAAAATTTCC
* * *
52456164 CGTG-TTTCAAAAATTTTCTTGTTTTAAAAAATTCT
1 CGTGTTTTCAAAAA-TTTCGTG-TTTCAAAAATCCT
52456199 CGTGTTTTCAAAAATTTCAGTGTTTCAAAAATTCC-
1 CGTGTTTTCAAAAATTTC-GTGTTTCAAAAA-TCCT
**
52456234 CGTGTTTT-AAAAATTTCTGTGTTTTCAAAAATTTT
1 CGTGTTTTCAAAAATTTC-GTG-TTTCAAAAATCCT
* * *
52456269 CGTATTTTCAAAAAAAAATTCGTGTTTCAAAAATCCA
1 CGTGTTTTC---AAAAATTTCGTGTTTCAAAAATCCT
*
52456306 CGTGTTTTCAAAAATTTCGGTGTTTCAAAAATCTT
1 CGTGTTTTCAAAAATTTC-GTGTTTCAAAAATCCT
* * **
52456341 CGTGTTTTCAAAAATTCCGGTGATTC-AAAATTTT
1 CGTGTTTTCAAAAATTTC-GTGTTTCAAAAATCCT
*
52456375 CGTGTTTTCTAAAAATTTCTGTGCTTCAAAAA
1 CGTGTTTTC-AAAAATTTC-GTGTTTCAAAAA
52456407 AATTTCGATT
Statistics
Matches: 175, Mismatches: 21, Indels: 23
0.80 0.10 0.11
Matches are distributed among these distances:
34 37 0.21
35 92 0.53
36 17 0.10
37 18 0.10
38 3 0.02
39 8 0.05
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
CGTGTTTTCAAAAATTTCGTGTTTCAAAAATCCT
Found at i:52456511 original size:16 final size:17
Alignment explanation
Indices: 52456491--52456570 Score: 74
Period size: 17 Copynumber: 4.7 Consensus size: 17
52456481 TTGCGTTTTG
52456491 AAAAATTCTCGTGTTTC
1 AAAAATTCTCGTGTTTC
* *
52456508 AAAAATTGTCGTGTTTTAA
1 AAAAATTCTCGTG-TTT-C
*
52456527 AAAAATTTTCGTGTTTC
1 AAAAATTCTCGTGTTTC
* * *
52456544 TAAAATTTTCATG-TTC
1 AAAAATTCTCGTGTTTC
52456560 AAAAATT-TCGT
1 AAAAATTCTCGT
52456571 TTTTTTTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
15 3 0.06
16 9 0.17
17 23 0.43
18 6 0.11
19 12 0.23
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTC
Found at i:52456532 original size:19 final size:19
Alignment explanation
Indices: 52456491--52456548 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
52456481 TTGCGTTTTG
*
52456491 AAAAATTCTCGTG-TTT-C
1 AAAAATTCTCGTGTTTTAA
*
52456508 AAAAATTGTCGTGTTTTAA
1 AAAAATTCTCGTGTTTTAA
*
52456527 AAAAATTTTCGTGTTTCTAA
1 AAAAATTCTCGTGTTT-TAA
52456547 AA
1 AA
52456549 TTTTCATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.34
18 3 0.09
19 15 0.43
20 5 0.14
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (19 bp):
AAAAATTCTCGTGTTTTAA
Found at i:52457437 original size:36 final size:38
Alignment explanation
Indices: 52457370--52457452 Score: 118
Period size: 36 Copynumber: 2.2 Consensus size: 38
52457360 ATAATAAATA
52457370 TTTATTTTTTATTTTTAAAAATATTTAAAAAT-A-TTT
1 TTTATTTTTTATTTTTAAAAATATTTAAAAATAAGTTT
*
52457406 TTTATTTTTTATTTTT-AAAATATTTTTAAAATAAGTTT
1 TTTATTTTTTATTTTTAAAAATA-TTTAAAAATAAGTTT
*
52457444 TTTAATTTT
1 TTTATTTTT
52457453 CTAAAATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 6 0.14
36 24 0.57
37 1 0.02
38 11 0.26
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (38 bp):
TTTATTTTTTATTTTTAAAAATATTTAAAAATAAGTTT
Found at i:52458905 original size:10 final size:9
Alignment explanation
Indices: 52458890--52458938 Score: 62
Period size: 10 Copynumber: 5.2 Consensus size: 9
52458880 AAATCAAAAT
*
52458890 AATTTTCAA
1 AATTTTTAA
52458899 AATTTTTAA
1 AATTTTTAA
52458908 ATATTTTTAA
1 A-ATTTTTAA
52458918 ATATTTTTAA
1 A-ATTTTTAA
*
52458928 AATTTTCAA
1 AATTTTTAA
52458937 AA
1 AA
52458939 AAAATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
9 18 0.49
10 19 0.51
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (9 bp):
AATTTTTAA
Found at i:52458909 original size:20 final size:20
Alignment explanation
Indices: 52458886--52458938 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
52458876 AAAAAAATCA
52458886 AAATAATTTTCAAAATTTTT
1 AAATAATTTTCAAAATTTTT
*
52458906 AAAT-ATTTTTAAATATTTTT
1 AAATAATTTTCAAA-ATTTTT
52458926 -AA-AATTTTCAAAA
1 AAATAATTTTCAAAA
52458939 AAAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 18 0.62
20 10 0.34
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATTTTCAAAATTTTT
Found at i:52462914 original size:14 final size:13
Alignment explanation
Indices: 52462881--52462911 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
52462871 TAAATTAATT
52462881 TTTTAA-TAAAAA
1 TTTTAATTAAAAA
52462893 TTTTAATTAAAAA
1 TTTTAATTAAAAA
52462906 TTTTAA
1 TTTTAA
52462912 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAATTAAAAA
Found at i:52463934 original size:29 final size:29
Alignment explanation
Indices: 52463889--52463951 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
52463879 ATTAGATTTG
* *
52463889 AAATTTTAAAATTTAAAAATA-AAGTGATT
1 AAATTTTAAAATATAAAAATATAA-AGATT
52463918 AAATTTCTAAAA-ATAAAAATATAAAGATT
1 AAATTT-TAAAATATAAAAATATAAAGATT
52463947 AAATT
1 AAATT
52463952 ACAAATATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (29 bp):
AAATTTTAAAATATAAAAATATAAAGATT
Found at i:52471068 original size:33 final size:33
Alignment explanation
Indices: 52471030--52471098 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
52471020 TTGATCATTT
52471030 CTATTTAAAAAAAATTCTGCGTGACCATTTAAG
1 CTATTTAAAAAAAATTCTGCGTGACCATTTAAG
52471063 CTATTTAAAAAAAATTCTGCGTGACCATTTAAG
1 CTATTTAAAAAAAATTCTGCGTGACCATTTAAG
52471096 CTA
1 CTA
52471099 ATCAAATGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (33 bp):
CTATTTAAAAAAAATTCTGCGTGACCATTTAAG
Found at i:52472388 original size:17 final size:17
Alignment explanation
Indices: 52472349--52472382 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
52472339 CTCTTCCTCC
52472349 GATTTCTTCTCATCTAG
1 GATTTCTTCTCATCTAG
52472366 GATTTCTTCTCATCTAG
1 GATTTCTTCTCATCTAG
52472383 CGTTTCAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.47
Consensus pattern (17 bp):
GATTTCTTCTCATCTAG
Found at i:52472878 original size:9 final size:9
Alignment explanation
Indices: 52472866--52472960 Score: 129
Period size: 9 Copynumber: 10.4 Consensus size: 9
52472856 AAATAAAAAA
52472866 AATTCGGGT
1 AATTCGGGT
52472875 AATTCGGGT
1 AATTCGGGT
*
52472884 ATTTTTC-GGT
1 A--ATTCGGGT
*
52472894 AATTCGGTT
1 AATTCGGGT
*
52472903 AATTCGGTT
1 AATTCGGGT
52472912 AATTCGGGT
1 AATTCGGGT
*
52472921 AATTCGGTT
1 AATTCGGGT
52472930 AATTCGGGT
1 AATTCGGGT
52472939 AATTCGGGT
1 AATTCGGGT
52472948 AATTCGGGT
1 AATTCGGGT
52472957 AATT
1 AATT
52472961 TTTAACCAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
8 3 0.04
9 67 0.87
10 4 0.05
11 3 0.04
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:52474072 original size:36 final size:36
Alignment explanation
Indices: 52474015--52474084 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
52474005 ACTAACTAAT
* *
52474015 GTAAACCATAAACCCCTAACCCCTATCCCCTAAATC
1 GTAAAACATAAACCCCTAACCCCTAACCCCTAAATC
* *
52474051 GTAAAACATAAA-CCGTAAACCCCTAACCCTTAAA
1 GTAAAACATAAACCCCT-AACCCCTAACCCCTAAA
52474085 CCCCAACCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.10
36 26 0.90
ACGTcount: A:0.41, C:0.36, G:0.04, T:0.19
Consensus pattern (36 bp):
GTAAAACATAAACCCCTAACCCCTAACCCCTAAATC
Found at i:52474093 original size:14 final size:15
Alignment explanation
Indices: 52474066--52474096 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
52474056 ACATAAACCG
52474066 TAAACCCCTAACCCT
1 TAAACCCCTAACCCT
52474081 TAAACCCC-AACCCT
1 TAAACCCCTAACCCT
52474095 TA
1 TA
52474097 TAACTGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAACCCCTAACCCT
Found at i:52475329 original size:41 final size:41
Alignment explanation
Indices: 52475221--52475425 Score: 245
Period size: 41 Copynumber: 5.0 Consensus size: 41
52475211 TATGATAAAT
* *
52475221 CTGAGCATTAGCGGCGCTTCTTCATAAACGCCGCTAAA--A
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
* *
52475260 ATAGAGTATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
1 CT-GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
* * *
52475302 CTGAGCACTAGTGGCGCTTCTTTAAAAACGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
*
52475343 CTAAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAG-C
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
* * * * * *
52475383 CTCGAGCATTAGAGGCACTTTTTAAAAAAAGCCGCTAATGCC
1 CT-GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
52475425 C
1 C
52475426 CCAAAAACTC
Statistics
Matches: 141, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 37 0.26
41 100 0.71
42 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
Found at i:52475512 original size:39 final size:38
Alignment explanation
Indices: 52475476--52475608 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 38
52475466 CGCTTTTTGG
52475476 AAAACGCCGCTAATGCTCATTTTTAGTGGCGTTTTTTA
1 AAAACGCCGCTAATGCTCATTTTTAGTGGCGTTTTTTA
* * * * * *
52475514 AAAAGTGCAGCTAATACTCGATCTTTAGTGACGTTTTTTTT
1 AAAA-CGCCGCTAATGCTC-ATTTTTAGTGGCG-TTTTTTA
* * *
52475555 AAAGCGCCACTAATGCTTGATTTTTAGTGGCGTTTTTTA
1 AAAACGCCGCTAATGC-TCATTTTTAGTGGCGTTTTTTA
*
52475594 TCCAAACGCCGCTAA
1 --AAAACGCCGCTAA
52475609 AAGCCTGTTT
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
38 4 0.06
39 17 0.24
40 30 0.42
41 20 0.28
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (38 bp):
AAAACGCCGCTAATGCTCATTTTTAGTGGCGTTTTTTA
Found at i:52475549 original size:40 final size:41
Alignment explanation
Indices: 52475476--52475593 Score: 138
Period size: 40 Copynumber: 3.0 Consensus size: 41
52475466 CGCTTTTTGG
52475476 AAAA-CGCC-GCTAATGCTC-ATTTTTAGTGGCGTTTTTTA
1 AAAAGCGCCAGCTAATGCTCGATTTTTAGTGGCGTTTTTTA
* * * * *
52475514 AAAAGTG-CAGCTAATACTCGATCTTTAGTGACGTTTTTTT
1 AAAAGCGCCAGCTAATGCTCGATTTTTAGTGGCGTTTTTTA
* *
52475554 TAAAGCGCCA-CTAATGCTTGATTTTTAGTGGCGTTTTTTA
1 AAAAGCGCCAGCTAATGCTCGATTTTTAGTGGCGTTTTTTA
52475594 TCCAAACGCC
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
38 5 0.08
39 10 0.16
40 47 0.73
41 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (41 bp):
AAAAGCGCCAGCTAATGCTCGATTTTTAGTGGCGTTTTTTA
Found at i:52481221 original size:5 final size:5
Alignment explanation
Indices: 52481211--52481236 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52481201 TGAGCATTCG
52481211 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
52481237 AATTTTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:52482277 original size:9 final size:9
Alignment explanation
Indices: 52482263--52482299 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52482253 TATAGTTGGA
52482263 TATTCGAAT
1 TATTCGAAT
52482272 TATTCGAAT
1 TATTCGAAT
*
52482281 TATTCGAGT
1 TATTCGAAT
52482290 TATTCGAAT
1 TATTCGAAT
52482299 T
1 T
52482300 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Done.