Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 17 of 26
Found at i:2352414 original size:28 final size:26
Alignment explanation
Indices: 2352382--2352433 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 26
2352372 ATTTAAAAAG
2352382 TAAATT-ATTTTGTATATACAATATTTTT
1 TAAATTGATTTT-T-TAT-CAATATTTTT
2352410 TAAATTGATTTTTTATCAATATTT
1 TAAATTGATTTTTTATCAATATTT
2352434 GTACTGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 8 0.35
27 3 0.13
28 7 0.30
29 5 0.22
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (26 bp):
TAAATTGATTTTTTATCAATATTTTT
Found at i:2353603 original size:22 final size:22
Alignment explanation
Indices: 2353578--2353625 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
2353568 TTTTATTAGA
*
2353578 AATGGATGATTATTTT-TTTTAT
1 AATGGATG-TAATTTTATTTTAT
*
2353600 AATGTATGTAATTTTAATTTTAT
1 AATGGATGTAATTTT-ATTTTAT
2353623 AAT
1 AAT
2353626 AAATTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 7 0.32
23 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (22 bp):
AATGGATGTAATTTTATTTTAT
Found at i:2355903 original size:145 final size:146
Alignment explanation
Indices: 2355680--2355965 Score: 441
Period size: 145 Copynumber: 2.0 Consensus size: 146
2355670 TCTAGTTTTG
* * * *
2355680 TTGTAGTTCATGATTGTTGAACGCAGCTTTGTAAGTTTTTTTCTTTGATAACGATATCAACCCTG
1 TTGTAGTTCATAATTGCTGAACGCAGCTTTGTAAGTCTTTTTCTTTGATAACAATATCAACCCTG
* * *
2355745 TATTCAATTTGGTTGCTTGCAGAAAATTCTGCCTGTCTTCATAGACAACCTAGTTTCTATGAATG
66 TATTCAATTTGGTTGCTCGCAGAAAATTCTGCATGTCTTCATAGACAACCAAGTTTCTATGAATG
*
2355810 GTTTGCATAATTAACC
131 ATTTGCATAATTAACC
* * *
2355826 TTGTAGTTTATAATTGCTGACCGCAGCTTTGTAAG-CTTTTTCTTTGATAACAATATCAACCTTG
1 TTGTAGTTCATAATTGCTGAACGCAGCTTTGTAAGTCTTTTTCTTTGATAACAATATCAACCCTG
2355890 TATTC-ATTGTGGTTGCTCGCAGAAAATTCTGCATGTCTTCATAGACAACCAAGTTTCTATGAAT
66 TATTCAATT-TGGTTGCTCGCAGAAAATTCTGCATGTCTTCATAGACAACCAAGTTTCTATGAAT
*
2355954 GATTTGCGTAAT
130 GATTTGCATAAT
2355966 CTATTTGAAA
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
144 3 0.02
145 93 0.73
146 31 0.24
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (146 bp):
TTGTAGTTCATAATTGCTGAACGCAGCTTTGTAAGTCTTTTTCTTTGATAACAATATCAACCCTG
TATTCAATTTGGTTGCTCGCAGAAAATTCTGCATGTCTTCATAGACAACCAAGTTTCTATGAATG
ATTTGCATAATTAACC
Found at i:2357537 original size:16 final size:15
Alignment explanation
Indices: 2357507--2357556 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
2357497 ATATTTAATT
2357507 TTTTAAAAAATTTATA
1 TTTTAAAAAA-TTATA
2357523 TATTTAAAAAATTAT-
1 T-TTTAAAAAATTATA
**
2357538 TTTTAAATTATTATA
1 TTTTAAAAAATTATA
2357553 TTTT
1 TTTT
2357557 TATACTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 11 0.37
15 5 0.17
16 5 0.17
17 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTAAAAAATTATA
Found at i:2357873 original size:15 final size:15
Alignment explanation
Indices: 2357853--2357882 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2357843 TATTTATATT
2357853 TAAAAATATGTTAAA
1 TAAAAATATGTTAAA
*
2357868 TAAAAATATTTTAAA
1 TAAAAATATGTTAAA
2357883 AATTAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TAAAAATATGTTAAA
Found at i:2358259 original size:2 final size:2
Alignment explanation
Indices: 2358252--2358290 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2358242 TCCTTCAAAT
2358252 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
2358291 TCTAAATTCT
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
Found at i:2358713 original size:4 final size:4
Alignment explanation
Indices: 2358697--2358753 Score: 78
Period size: 4 Copynumber: 13.8 Consensus size: 4
2358687 TTCTGGTATT
*
2358697 TTTC TTCC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTCATC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT--TC TTTC
*
2358747 TCTC TTT
1 TTTC TTT
2358754 TAGATTCTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
4 43 0.91
6 4 0.09
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:2359634 original size:51 final size:51
Alignment explanation
Indices: 2359558--2359658 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
2359548 TTTATTTAAA
2359558 TTTAGTTATTATTATTAACATTGATATGAACTTTGGGGATAAGTTTGAACT
1 TTTAGTTATTATTATTAACATTGATATGAACTTTGGGGATAAGTTTGAACT
2359609 TTTAGTTATTATTATTAACATTGATATGAACTTTGGGGATAAGTTTGAAC
1 TTTAGTTATTATTATTAACATTGATATGAACTTTGGGGATAAGTTTGAAC
2359659 CTTGATAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.45
Consensus pattern (51 bp):
TTTAGTTATTATTATTAACATTGATATGAACTTTGGGGATAAGTTTGAACT
Found at i:2360326 original size:2 final size:2
Alignment explanation
Indices: 2360321--2360362 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2360311 AGAGATTCAC
2360321 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
2360363 ACAGTTTGAC
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:2361151 original size:68 final size:68
Alignment explanation
Indices: 2361039--2361171 Score: 230
Period size: 68 Copynumber: 2.0 Consensus size: 68
2361029 TCGAAAGCAA
2361039 TCTCTTTCAATATGCAACGCATATATGTTTTAAATATGTCAAACATAGTGGATAATGCACCAATA
1 TCTCTTTCAATATGCAACGCATATATGTTTTAAATATGTCAAACATAGTGGATAATGCACCAATA
2361104 CCT
66 CCT
* * * *
2361107 TCTCTTTCAATGTGCAACGCATGTATGTTTTAAATATGTGAAACATAGTGGATAATGCCCCAATA
1 TCTCTTTCAATATGCAACGCATATATGTTTTAAATATGTCAAACATAGTGGATAATGCACCAATA
2361172 ACTACAGCCT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (68 bp):
TCTCTTTCAATATGCAACGCATATATGTTTTAAATATGTCAAACATAGTGGATAATGCACCAATA
CCT
Found at i:2366737 original size:18 final size:18
Alignment explanation
Indices: 2366716--2366751 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2366706 TTAATTTTTT
2366716 TTATATTAT-TAAATATTA
1 TTATATTATATAAA-ATTA
2366734 TTATATTATATAAAATTA
1 TTATATTATATAAAATTA
2366752 AATATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATATTATATAAAATTA
Found at i:2366767 original size:27 final size:26
Alignment explanation
Indices: 2366722--2366781 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
2366712 TTTTTTATAT
*
2366722 TATTAAATATTATTATATTATATAAA
1 TATTAAATATTAATATATTATATAAA
*
2366748 -ATTAAATATATAATATTATTATGTAAA
1 TATTAAATAT-TAATA-TATTATATAAA
2366775 TATTAAA
1 TATTAAA
2366782 AAAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 9 0.31
26 4 0.14
27 10 0.34
28 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TATTAAATATTAATATATTATATAAA
Found at i:2368352 original size:23 final size:24
Alignment explanation
Indices: 2368321--2368382 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
2368311 AAATTAAATT
*
2368321 AAATTATATAAATATT-AATAAAA
1 AAATAATATAAATATTAAATAAAA
* * *
2368344 AAATAATATAATTTTTAAATAATA
1 AAATAATATAAATATTAAATAAAA
2368368 AAATAAATTATAAAT
1 AAAT-AA-TATAAAT
2368383 TAAATCAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 13 0.42
24 10 0.32
25 2 0.06
26 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATAATATAAATATTAAATAAAA
Found at i:2368518 original size:16 final size:16
Alignment explanation
Indices: 2368499--2368529 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2368489 GTTTAAATTA
2368499 AAAAATATTTATTTAT
1 AAAAATATTTATTTAT
*
2368515 AAAATTATTTATTTA
1 AAAAATATTTATTTA
2368530 ATATTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAAAATATTTATTTAT
Found at i:2368583 original size:12 final size:13
Alignment explanation
Indices: 2368560--2368615 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 13
2368550 AAAAATATTT
2368560 AATTTAAAATATA
1 AATTTAAAATATA
2368573 AATTT-AAATATA
1 AATTTAAAATATA
*
2368585 AA-TTAAAGT-T-
1 AATTTAAAATATA
*
2368595 -ATTTAAAAAATA
1 AATTTAAAATATA
2368607 AA-TTAAAAT
1 AATTTAAAAT
2368616 TTTCTCTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
9 1 0.03
10 5 0.15
11 4 0.12
12 18 0.53
13 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
AATTTAAAATATA
Found at i:2368821 original size:25 final size:24
Alignment explanation
Indices: 2368784--2368873 Score: 71
Period size: 25 Copynumber: 3.8 Consensus size: 24
2368774 GAATTTAAAA
2368784 TTTAATAAAAAATTAAATTATATAT
1 TTTAA-AAAAAATTAAATTATATAT
*
2368809 TTTAAAAATAAATTAAA--A-ATAA
1 TTTAAAAA-AAATTAAATTATATAT
* *
2368831 GTTAAATAAAATTTAAAATT-TATAT
1 TTTAAA-AAAAATT-AAATTATATAT
**
2368856 TTTAAATTAAATTAAATT
1 TTTAAAAAAAATTAAATT
2368874 TTAAAAATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
22 12 0.24
23 11 0.22
24 7 0.14
25 21 0.41
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (24 bp):
TTTAAAAAAAATTAAATTATATAT
Found at i:2368889 original size:17 final size:17
Alignment explanation
Indices: 2368859--2368903 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
2368849 TTTATATTTT
*
2368859 AAATTAAATTAAATTTTAA
1 AAATTAAA--AAATTTAAA
2368878 AAATTAAAAAATTTAAA
1 AAATTAAAAAATTTAAA
2368895 AAATTAAAA
1 AAATTAAAA
2368904 TTATATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 17 0.68
19 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTAAAAAATTTAAA
Found at i:2368934 original size:22 final size:23
Alignment explanation
Indices: 2368900--2368943 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
2368890 TTAAAAAATT
*
2368900 AAAATTATATTTAAATTTAGTAA
1 AAAATCATATTTAAATTTAGTAA
**
2368923 AAAATCAT-TTTATTTTTAGTA
1 AAAATCATATTTAAATTTAGTA
2368944 TATTATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
AAAATCATATTTAAATTTAGTAA
Found at i:2368958 original size:22 final size:23
Alignment explanation
Indices: 2368933--2368998 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
2368923 AAAATCATTT
* *
2368933 TATTTTTAGTA-TATTATTAAAA
1 TATTTTTAATATTAATATTAAAA
2368955 TA-TTTTAATATTAATATTAAAA
1 TATTTTTAATATTAATATTAAAA
*
2368977 TATTATTTAAATATAAATATTA
1 TATT-TTT-AATATTAATATTA
2368999 TTTTTATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.19
22 14 0.38
23 1 0.03
24 3 0.08
25 12 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTTTTAATATTAATATTAAAA
Found at i:2369012 original size:19 final size:18
Alignment explanation
Indices: 2368967--2369015 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
2368957 TTTTAATATT
2368967 AATATTAAAATATTATTTA
1 AATATT-AAATATTATTTA
*
2368986 AATA-TAAATATTATTTTT
1 AATATTAAATATTA-TTTA
*
2369004 ATTATTAAATAT
1 AATATTAAATAT
2369016 AATACTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 8 0.31
18 7 0.27
19 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATTAAATATTATTTA
Found at i:2377028 original size:13 final size:13
Alignment explanation
Indices: 2377012--2377097 Score: 62
Period size: 13 Copynumber: 7.0 Consensus size: 13
2377002 TTTTATATTT
2377012 ATATTATTTTTTA
1 ATATTATTTTTTA
*
2377025 ATA-T-TTTTATA
1 ATATTATTTTTTA
2377036 ATA-TATTTTTATA
1 ATATTATTTTT-TA
*
2377049 A-ATTTATTTATTA
1 ATA-TTATTTTTTA
*
2377062 ATATTATGTTTTA
1 ATATTATTTTTTA
2377075 A-A--ATTTTTT-
1 ATATTATTTTTTA
2377084 ATATTATATTTTTA
1 ATATTAT-TTTTTA
2377098 TTTTATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
9 1 0.02
10 7 0.12
11 10 0.18
12 9 0.16
13 23 0.40
14 7 0.12
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (13 bp):
ATATTATTTTTTA
Found at i:2377056 original size:14 final size:13
Alignment explanation
Indices: 2377025--2377098 Score: 68
Period size: 13 Copynumber: 5.8 Consensus size: 13
2377015 TTATTTTTTA
2377025 ATATTTTTATAAT
1 ATATTTTTATAAT
2377038 ATATTTTTATAA-
1 ATATTTTTATAAT
2377050 AT-TTATTTATTAAT
1 ATATT-TTTA-TAAT
2377064 ATTATGTTTTA-AA-
1 A-TAT-TTTTATAAT
*
2377077 AT-TTTTTATATT
1 ATATTTTTATAAT
2377089 ATATTTTTAT
1 ATATTTTTAT
2377099 TTTATAAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 18
0.73 0.01 0.26
Matches are distributed among these distances:
10 5 0.10
11 4 0.08
12 9 0.18
13 23 0.45
14 3 0.06
15 1 0.02
16 5 0.10
17 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (13 bp):
ATATTTTTATAAT
Found at i:2377094 original size:37 final size:36
Alignment explanation
Indices: 2377009--2377097 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 36
2376999 TTATTTTATA
2377009 TTTATATTAT-TTTTTAATATTTTTATAATATATTT
1 TTTATATTATATTTTTAATATTTTTATAATATATTT
* *
2377044 TTATAAATT-TATTTATTAATATTATGTTTTAA-A-ATTT
1 TT-TATATTATATTT-TTAATATT-T-TTATAATATATTT
2377081 TTTATATTATATTTTTA
1 TTTATATTATATTTTTA
2377098 TTTTATAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
35 3 0.07
36 16 0.36
37 19 0.42
38 2 0.04
39 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (36 bp):
TTTATATTATATTTTTAATATTTTTATAATATATTT
Found at i:2377098 original size:13 final size:13
Alignment explanation
Indices: 2377002--2377104 Score: 58
Period size: 13 Copynumber: 7.9 Consensus size: 13
2376992 TACCTATTTA
2377002 TTTTATATTTATAT
1 TTTTATA-TTATAT
2377016 TATTT-T-TTAATAT
1 T-TTTATATT-ATAT
*
2377029 TTTTATAATATAT
1 TTTTATATTATAT
2377042 TTTTATAAATT-TAT
1 TTTTAT--ATTATAT
*
2377056 TTATTAATATTAT-G
1 TT-TT-ATATTATAT
*
2377070 TTTTA-A-AAT-T
1 TTTTATATTATAT
2377080 TTTTATATTATAT
1 TTTTATATTATAT
*
2377093 TTTTATTTTATA
1 TTTTATATTATA
2377105 AATATATCAT
Statistics
Matches: 70, Mismatches: 7, Indels: 25
0.69 0.07 0.25
Matches are distributed among these distances:
10 7 0.10
11 2 0.03
12 8 0.11
13 30 0.43
14 13 0.19
15 8 0.11
16 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (13 bp):
TTTTATATTATAT
Found at i:2377117 original size:51 final size:48
Alignment explanation
Indices: 2377000--2377104 Score: 124
Period size: 50 Copynumber: 2.2 Consensus size: 48
2376990 AATACCTATT
* * *
2377000 TATTT-TATATTTATATTATTTTTTAATATTTTTATAATATATTTTTA
1 TATTTATATATTAATATTATGTTTTAAAATTTTTATAATATATTTTTA
* *
2377047 TAAATTTATTTATTAATATTATGTTTTAAAATTTTTTATATTATATTTTTA
1 T--ATTTATATATTAATATTATGTTTTAAAA-TTTTTATAATATATTTTTA
2377098 T-TTTATA
1 TATTTATA
2377105 AATATATCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
47 1 0.02
48 5 0.10
49 4 0.08
50 19 0.40
51 19 0.40
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (48 bp):
TATTTATATATTAATATTATGTTTTAAAATTTTTATAATATATTTTTA
Found at i:2377685 original size:43 final size:45
Alignment explanation
Indices: 2377637--2377725 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 45
2377627 TTTATAATTT
2377637 AAATAATATTAAAATATT-AATAAAT-ATTT-TT-ATATTAATATAA
1 AAATAATATTAAAAT-TTAAATAAATAATTTATTAATATTAA-ATAA
*
2377680 AAATAATATTTAAATTTAAATAAATAATTTATTAATATTAAATAA
1 AAATAATATTAAAATTTAAATAAATAATTTATTAATATTAAATAA
2377725 A
1 A
2377726 TATTTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
42 2 0.05
43 21 0.51
44 4 0.10
45 7 0.17
46 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (45 bp):
AAATAATATTAAAATTTAAATAAATAATTTATTAATATTAAATAA
Found at i:2377736 original size:22 final size:22
Alignment explanation
Indices: 2377649--2377736 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 22
2377639 ATAATATTAA
2377649 AATATT-AATAAAT-A-TTTTT
1 AATATTAAATAAATAATTTTTT
* *
2377668 -ATATTAATATAAAAATAATATTTA
1 AATATTAA-AT--AAATAATTTTTT
*
2377692 AAT-TTAAATAAATAATTTATT
1 AATATTAAATAAATAATTTTTT
*
2377713 AATATTAAATAAATATTTTTTT
1 AATATTAAATAAATAATTTTTT
2377735 AA
1 AA
2377737 CTTTAATTGT
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
18 5 0.09
19 1 0.02
20 2 0.04
21 12 0.22
22 22 0.41
23 3 0.06
24 7 0.13
25 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTAAATAAATAATTTTTT
Found at i:2379017 original size:2 final size:2
Alignment explanation
Indices: 2379010--2379038 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2379000 TACTGGCAAT
2379010 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
2379039 GTTATTATTT
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:2382225 original size:27 final size:26
Alignment explanation
Indices: 2382173--2382246 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 26
2382163 TTCTGAAGAG
*
2382173 TAAAAATATTTTTTAATTATTTATTTATTTA
1 TAAAAATATTTTTTAA-TA-TT-TTTA--AA
*
2382204 TAAAATTATATTTTTAATATTTTTAAA
1 TAAAAATAT-TTTTTAATATTTTTAAA
2382231 TAAAAATATTTTTTAA
1 TAAAAATATTTTTTAA
2382247 ATCTGATCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 7 0.18
27 9 0.23
29 4 0.10
30 2 0.05
31 10 0.26
32 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TAAAAATATTTTTTAATATTTTTAAA
Found at i:2382436 original size:22 final size:21
Alignment explanation
Indices: 2382410--2382455 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2382400 TAAGTATTTT
2382410 ATTATATTATAATCATATATAA
1 ATTATATTATAATCAT-TATAA
* * *
2382432 ATTATTTTATATTTATTATAA
1 ATTATATTATAATCATTATAA
2382453 ATT
1 ATT
2382456 TTGATACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATATTATAATCATTATAA
Found at i:2382489 original size:15 final size:15
Alignment explanation
Indices: 2382469--2382528 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
2382459 ATACGTTAAT
2382469 AATTTATATTATATA
1 AATTTATATTATATA
* *
2382484 AATTTAAATT-TGAGA
1 AATTTATATTAT-ATA
*
2382499 CATTTTATATTGATATTA
1 -AATTTATATT-ATA-TA
2382517 AATTTATATTAT
1 AATTTATATTAT
2382529 TTTTTATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
14 1 0.03
15 11 0.32
16 10 0.29
17 10 0.29
18 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (15 bp):
AATTTATATTATATA
Found at i:2382555 original size:28 final size:30
Alignment explanation
Indices: 2382500--2382566 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
2382490 AATTTGAGAC
2382500 ATTTTATATTGATATTAAATTTATATTATT
1 ATTTTATATTGATATTAAATTTATATTATT
* *
2382530 -TTTTATATT-ATCTTATATTT-TAATTATT
1 ATTTTATATTGATATTAAATTTAT-ATTATT
2382558 ATTTT-TATT
1 ATTTTATATT
2382567 TGTGGCAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 1 0.03
28 19 0.58
29 13 0.39
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (30 bp):
ATTTTATATTGATATTAAATTTATATTATT
Found at i:2383024 original size:13 final size:13
Alignment explanation
Indices: 2382975--2383025 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
2382965 TAGAAAATCC
* *
2382975 ATATATATATATAT
1 ATATGTATATA-AA
2382989 ATAT-TATATAAA
1 ATATGTATATAAA
*
2383001 ATTATGCATATAAA
1 A-TATGTATATAAA
2383015 ATATGTATATA
1 ATATGTATATA
2383026 TAACACTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 2 0.06
13 18 0.56
14 12 0.38
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (13 bp):
ATATGTATATAAA
Found at i:2383519 original size:18 final size:17
Alignment explanation
Indices: 2383498--2383542 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2383488 TTAAATTAGA
*
2383498 TAAATTTAAATAATTATT
1 TAAATTTAAA-AAATATT
*
2383516 TAAATAATAAAAAATATT
1 TAAAT-TTAAAAAATATT
2383534 TAAATTTAA
1 TAAATTTAA
2383543 TTATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 16 0.70
19 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAAAAATATT
Found at i:2383550 original size:22 final size:22
Alignment explanation
Indices: 2383520--2383574 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
2383510 ATTATTTAAA
*
2383520 TAATA-AAAAATATTTAAAT-T
1 TAATATAAAAATATATAAATAT
2383540 TAAT-TATAAAATATATAAATAT
1 TAATATA-AAAATATATAAATAT
2383562 TAATATAAAAATA
1 TAATATAAAAATA
2383575 ATATTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.17
21 12 0.40
22 11 0.37
23 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATATAAAAATATATAAATAT
Found at i:2383555 original size:23 final size:23
Alignment explanation
Indices: 2383513--2383587 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
2383503 TTAAATAATT
* *
2383513 ATTTAAATAATAAAAAATATTTAA
1 ATTT-AATTATAAAATATATTTAA
2383537 ATTTAATTATAAAATATA--TAA
1 ATTTAATTATAAAATATATTTAA
*
2383558 ATATTAA-TATAAAAATAATATTTTA
1 AT-TTAATTAT-AAAAT-ATATTTAA
2383583 ATTTA
1 ATTTA
2383588 GTCGAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 8 0.19
22 9 0.21
23 15 0.35
24 7 0.16
25 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAATTATAAAATATATTTAA
Found at i:2385250 original size:25 final size:25
Alignment explanation
Indices: 2385216--2385265 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2385206 TTTATTATCA
*
2385216 TAATAATTTAAAATTATTTTTAAAT
1 TAATAATTTAAAATTATATTTAAAT
* * *
2385241 TAATATTTTATATTTATATTTAAAT
1 TAATAATTTAAAATTATATTTAAAT
2385266 AAAAATATCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAATAATTTAAAATTATATTTAAAT
Found at i:2385273 original size:20 final size:21
Alignment explanation
Indices: 2385250--2385288 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2385240 TTAATATTTT
*
2385250 ATAT-TTATATTTAAATAAAA
1 ATATCTTATATTAAAATAAAA
*
2385270 ATATCTTTTATTAAAATAA
1 ATATCTTATATTAAAATAA
2385289 TAGTTCAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATCTTATATTAAAATAAAA
Found at i:2386934 original size:13 final size:14
Alignment explanation
Indices: 2386916--2386957 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2386906 TTTAATAAAT
2386916 TTAAAATAAT-ATA
1 TTAAAATAATAATA
2386929 TTAAAATATATAATA
1 TTAAAATA-ATAATA
* *
2386944 TCAAAATAAAAATA
1 TTAAAATAATAATA
2386958 ATTTATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.32
14 7 0.28
15 10 0.40
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAATAATAATA
Found at i:2387478 original size:15 final size:15
Alignment explanation
Indices: 2387460--2387502 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2387450 TATCATATAT
2387460 TTATATAT-TAAAAAA
1 TTATATATAT-AAAAA
*
2387475 TTATATATATTAAAA
1 TTATATATATAAAAA
*
2387490 TTATATTTATAAA
1 TTATATATATAAA
2387503 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 23 0.96
16 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATATATATAAAAA
Found at i:2387942 original size:27 final size:29
Alignment explanation
Indices: 2387889--2387950 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
2387879 AAAAAAATAA
*
2387889 TTAAAATATAAATATTAGTATATTAAACT
1 TTAAAATATAAATATTAATATATTAAACT
* * *
2387918 TTAAAATA-ATATTTTAATATA-TAAAGT
1 TTAAAATATAAATATTAATATATTAAACT
2387945 TTAAAA
1 TTAAAA
2387951 ACTCTGACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 11 0.38
28 10 0.34
29 8 0.28
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (29 bp):
TTAAAATATAAATATTAATATATTAAACT
Found at i:2387951 original size:28 final size:28
Alignment explanation
Indices: 2387889--2387951 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
2387879 AAAAAAATAA
*
2387889 TTAAAATATAAATATTAGTATATTAAACT
1 TTAAAA-ATAAATATTAATATATTAAACT
* *
2387918 TT-AAAATAATATTTTAATATA-TAAAGT
1 TTAAAAATAA-ATATTAATATATTAAACT
2387945 TTAAAAA
1 TTAAAAA
2387952 CTCTGACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 11 0.38
28 16 0.55
29 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (28 bp):
TTAAAAATAAATATTAATATATTAAACT
Found at i:2389158 original size:16 final size:17
Alignment explanation
Indices: 2389132--2389179 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2389122 TAATATTATA
2389132 TATATATATATAAAAATT
1 TATA-ATATATAAAAATT
*
2389150 T-TAATATATTAATAATT
1 TATAATATA-TAAAAATT
*
2389167 TATATTATATAAA
1 TATAATATATAAA
2389180 TTTTAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 5 0.20
17 13 0.52
18 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATAATATATAAAAATT
Found at i:2389158 original size:18 final size:18
Alignment explanation
Indices: 2389135--2389186 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 18
2389125 TATTATATAT
2389135 ATATATATAAAAATTTTA
1 ATATATATAAAAATTTTA
*
2389153 ATATAT-TAATAA-TTT-
1 ATATATATAAAAATTTTA
*
2389168 ATAT-TATATAAATTTTA
1 ATATATATAAAAATTTTA
2389185 AT
1 AT
2389187 TTATTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.04
15 8 0.29
16 6 0.21
17 7 0.25
18 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATAAAAATTTTA
Found at i:2389482 original size:2 final size:2
Alignment explanation
Indices: 2389433--2389462 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2389423 TGGAGCAACC
2389433 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
2389463 TAAAGTTAAT
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):
AT
Found at i:2390294 original size:17 final size:18
Alignment explanation
Indices: 2390252--2390294 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2390242 TAAAATTTTT
*
2390252 TAATTTAAATATAATAAA
1 TAATTTTAATATAATAAA
*
2390270 -AATATTAATATAA-AAA
1 TAATTTTAATATAATAAA
2390286 TAATTTTAA
1 TAATTTTAA
2390295 AATATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATTTTAATATAATAAA
Found at i:2390320 original size:25 final size:25
Alignment explanation
Indices: 2390215--2390322 Score: 91
Period size: 25 Copynumber: 4.4 Consensus size: 25
2390205 TTCATTCATT
* * *
2390215 TAATTTAAATTATT-ATTTAAATAT
1 TAATATAAAATATTAATTTAAATAA
* *
2390239 TAATA-AAATTTTTTAATTTAAAT-A
1 TAATATAAA-ATATTAATTTAAATAA
*
2390263 TAATA-AAAATATTAATATAAA-AA
1 TAATATAAAATATTAATTTAAATAA
* *
2390286 TAATTTTAAAATATTATTTTAAATAA
1 TAA-TATAAAATATTAATTTAAATAA
2390312 TAATATAAAAT
1 TAATATAAAAT
2390323 TAAGAGAATA
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
23 17 0.25
24 17 0.25
25 29 0.43
26 5 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAATATAAAATATTAATTTAAATAA
Found at i:2390661 original size:21 final size:21
Alignment explanation
Indices: 2390618--2390675 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2390608 AGTTAAAAAA
2390618 TTACT-ATA-TATTTTATTTAT
1 TTACTAATATTATTTT-TTTAT
*
2390638 TTATTAA-ATTATTTTTTTATT
1 TTACTAATATTATTTTTTTA-T
*
2390659 TTACTAATATAATTTTT
1 TTACTAATATTATTTTT
2390676 AAAATCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 9 0.29
21 14 0.45
22 8 0.26
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (21 bp):
TTACTAATATTATTTTTTTAT
Found at i:2390930 original size:17 final size:18
Alignment explanation
Indices: 2390882--2390931 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
2390872 AATTGATAAA
*
2390882 TTTATAAAAA-TAATTTT
1 TTTAAAAAAATTAATTTT
2390899 TTTAAATCAATAATTAA-TTT
1 TTTAAA--AA-AATTAATTTT
2390919 TTTAAAAAAATTA
1 TTTAAAAAAATTA
2390932 TATTATTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
17 10 0.36
18 2 0.07
19 2 0.07
20 11 0.39
21 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAAAAAAATTAATTTT
Found at i:2398285 original size:20 final size:20
Alignment explanation
Indices: 2398246--2398285 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2398236 CTTCGTATTT
*
2398246 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
2398266 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
2398286 TTTTGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:2398331 original size:25 final size:25
Alignment explanation
Indices: 2398297--2398367 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
2398287 TTTGATATAA
*
2398297 TAATAAATTTATATTATTTTAATTT
1 TAATATATTTATATTATTTTAATTT
*
2398322 TAATATATTTTTA-TA-TTT-ATTT
1 TAATATATTTATATTATTTTAATTT
*
2398344 T--T-TATTTATATTATTATATATTT
1 TAATATATTTATATTATTTTA-ATTT
2398367 T
1 T
2398368 TTTAATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 7 0.18
20 3 0.08
21 2 0.05
22 5 0.13
23 8 0.21
24 2 0.05
25 11 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TAATATATTTATATTATTTTAATTT
Found at i:2398345 original size:23 final size:23
Alignment explanation
Indices: 2398310--2398386 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
2398300 TAAATTTATA
*
2398310 TTAT-TTTAATTTTAATATATTT
1 TTATATTTATTTTTAATATATTT
* *
2398332 TTATATTTATTTTTTATTTATATTA
1 TTATATTTA-TTTTTA-ATATATTT
*
2398357 TTATATATT-TTTTTAATATTATAT
1 TTATAT-TTATTTTTAATA-TATTT
2398381 TTATAT
1 TTATAT
2398387 AATGTAGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
22 4 0.09
23 6 0.14
24 20 0.45
25 12 0.27
26 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTATATTTATTTTTAATATATTT
Found at i:2398369 original size:25 final size:26
Alignment explanation
Indices: 2398308--2398381 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 26
2398298 AATAAATTTA
*
2398308 TATTAT-TTTAATTTTAATA-TAT-T
1 TATTATATTTATTTTTAATATTATAT
*
2398331 T-TTATATTTATTTTTTAT-TTATAT
1 TATTATATTTATTTTTAATATTATAT
2398355 TATTATATATT-TTTTTAATATTATAT
1 TATTATAT-TTATTTTTAATATTATAT
2398381 T
1 T
2398382 TATATAATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
22 4 0.10
23 14 0.33
24 2 0.05
25 13 0.31
26 9 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TATTATATTTATTTTTAATATTATAT
Found at i:2398375 original size:21 final size:20
Alignment explanation
Indices: 2398335--2398378 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
2398325 TATATTTTTA
*
2398335 TATTTATTTTTTATTTATAT
1 TATTTATTTTTTATTAATAT
2398355 TATTATATATTTTT-TTAATAT
1 TATT-TAT-TTTTTATTAATAT
2398376 TAT
1 TAT
2398379 ATTTATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 12 0.57
22 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTATTTTTTATTAATAT
Found at i:2398376 original size:27 final size:28
Alignment explanation
Indices: 2398306--2398381 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
2398296 ATAATAAATT
* *
2398306 TATATTATTTTAAT-TTTA-ATATATTTT
1 TATATTTTTTTAATATTTATAT-TATTTA
*
2398333 TATATTTATTTT-TTATTTATATTA-TTA
1 TATATTT-TTTTAATATTTATATTATTTA
2398360 TATATTTTTTTAATA-TTATATT
1 TATATTTTTTTAATATTTATATT
2398382 TATATAATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
26 11 0.27
27 18 0.44
28 10 0.24
29 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
TATATTTTTTTAATATTTATATTATTTA
Found at i:2398384 original size:27 final size:26
Alignment explanation
Indices: 2398306--2398384 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 26
2398296 ATAATAAATT
* *
2398306 TATATTATTTTAATTTTAATATATTTTTA
1 TATATTTTTTTAA-TTT-ATAT-TTATTA
*
2398335 TAT-TTATTTTTTATTTATA-TTATTA
1 TATATT-TTTTTAATTTATATTTATTA
2398360 TATATTTTTTTAATATTATATTTAT
1 TATATTTTTTTAAT-TTATATTTAT
2398385 ATAATGTAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
25 15 0.36
26 7 0.17
27 7 0.17
28 5 0.12
29 8 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TATATTTTTTTAATTTATATTTATTA
Found at i:2398689 original size:103 final size:103
Alignment explanation
Indices: 2398551--2398740 Score: 285
Period size: 103 Copynumber: 1.8 Consensus size: 103
2398541 TTTTGTATAT
* * * *
2398551 ATAAGATTTAATTAAAACTACAATCGATATTATATTGATT-AAAAAATTATATTTTAATATATAT
1 ATAAAATTTAATTAAAACTACAATCAATATCATATTAATTCAAAAAA-TATATTTTAATATATAT
*
2398615 TTAATTATAAAATTTATTAATATTTGATAAAATTATAAA
65 TTAATCATAAAATTTATTAATATTTGATAAAATTATAAA
*
2398654 ATAAAATTTAATTAAATCTA-ATATCAATATCATATTAATTCAAAAAATATATTTTAATATATAT
1 ATAAAATTTAATTAAAACTACA-ATCAATATCATATTAATTCAAAAAATATATTTTAATATATAT
*
2398718 TTAATCATTAAATTTATTAATAT
65 TTAATCATAAAATTTATTAATAT
2398741 CCAATTAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
102 1 0.01
103 71 0.91
104 6 0.08
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (103 bp):
ATAAAATTTAATTAAAACTACAATCAATATCATATTAATTCAAAAAATATATTTTAATATATATT
TAATCATAAAATTTATTAATATTTGATAAAATTATAAA
Found at i:2398806 original size:6 final size:6
Alignment explanation
Indices: 2398795--2398824 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2398785 TAAATGTGTC
2398795 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
2398825 TTATTCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:2399189 original size:43 final size:44
Alignment explanation
Indices: 2399111--2399194 Score: 100
Period size: 43 Copynumber: 1.9 Consensus size: 44
2399101 TATTAAAAAA
*
2399111 TATTATTTTTATTAAAAAATATTTAAATTGAATT-AATTTAAAT
1 TATTATTTTTATTAAAAAATATTTAAATCGAATTAAATTTAAAT
* ** *
2399154 TATTATTTTTTTTAAAATTTATTTTAAA-CGGATTAAATTTA
1 TATTATTTTTATTAAAAAATA-TTTAAATCGAATTAAATTTA
2399195 TTAAATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 22 0.65
44 12 0.35
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (44 bp):
TATTATTTTTATTAAAAAATATTTAAATCGAATTAAATTTAAAT
Found at i:2399899 original size:2 final size:2
Alignment explanation
Indices: 2399894--2399918 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2399884 TTTGATGATT
2399894 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
2399919 CAATGTTAAT
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:2400343 original size:86 final size:84
Alignment explanation
Indices: 2400171--2400345 Score: 242
Period size: 84 Copynumber: 2.1 Consensus size: 84
2400161 CCACAGCAAG
* * * *
2400171 ATCAATTAATCTCTCGTCGAAAGCTTGTAGAATATCCTTCATATTCCTTTCACATTTTCTTGTTT
1 ATCAACTAATCTCTCATCGAAAGCTTGTAGAATATCCTTCACATTCCTTTCACATTTTCCTGTTT
2400236 TTACCCCCAAACCATTGGT
66 TTACCCCCAAACCATTGGT
* * * *
2400255 ATCAACTAATCTCTCATCGACAGCTTGTAGAATGTCCTTCACATTCCTCTTTCTCGTTTTCCTGT
1 ATCAACTAATCTCTCATCGAAAGCTTGTAGAATATCCTTCACATT-C-CTTTCACATTTTCCTGT
* *
2400320 TTTTTCCCCCAAACCCTTGGT
64 TTTTACCCCCAAACCATTGGT
2400341 ATCAA
1 ATCAA
2400346 AGTTTATAGC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 40 0.51
85 1 0.01
86 38 0.48
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.39
Consensus pattern (84 bp):
ATCAACTAATCTCTCATCGAAAGCTTGTAGAATATCCTTCACATTCCTTTCACATTTTCCTGTTT
TTACCCCCAAACCATTGGT
Found at i:2403098 original size:22 final size:21
Alignment explanation
Indices: 2403054--2403100 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
2403044 ATATTATGTC
* *
2403054 ATATTTTAATTATTTTATATT
1 ATATTTTAAATATTATATATT
*
2403075 ATATTTTAAAATATTATATTTT
1 ATATTTT-AAATATTATATATT
2403097 ATAT
1 ATAT
2403101 AATTTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTTTAAATATTATATATT
Found at i:2403339 original size:23 final size:20
Alignment explanation
Indices: 2403279--2403321 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2403269 CATAAAATTA
*
2403279 AATTAGTTTATATATTTATTT
1 AATTAATTTATAT-TTTATTT
2403300 AATTAATTTATA-TTTATTT
1 AATTAATTTATATTTTATTT
2403319 AAT
1 AAT
2403322 CTGATTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATTAATTTATATTTTATTT
Found at i:2404130 original size:23 final size:23
Alignment explanation
Indices: 2404099--2404153 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
2404089 TTAAAAAAAT
*
2404099 TATTTATTT-TATATATATATATA
1 TATTAATTTCTATATA-ATATATA
* *
2404122 TATTAATTTCTTTTTAATATATA
1 TATTAATTTCTATATAATATATA
*
2404145 TTTTAATTT
1 TATTAATTT
2404154 AATTTCACGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTAATTTCTATATAATATATA
Found at i:2404696 original size:25 final size:28
Alignment explanation
Indices: 2404641--2404692 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
2404631 AAAATTTTAG
*
2404641 TTATTAAATATATATATATAATGATTTA
1 TTATTAAATATATATATATAATGATTAA
2404669 TTATT-AATATA-ATATA-AAT-ATTAA
1 TTATTAAATATATATATATAATGATTAA
2404693 ATTAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.17
25 3 0.13
26 5 0.22
27 6 0.26
28 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TTATTAAATATATATATATAATGATTAA
Found at i:2405040 original size:17 final size:17
Alignment explanation
Indices: 2405018--2405055 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2405008 AACTATTATT
2405018 AATATTAATTATAATAA
1 AATATTAATTATAATAA
*
2405035 AATATTAATTATAATAT
1 AATATTAATTATAATAA
2405052 AATA
1 AATA
2405056 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATTAATTATAATAA
Found at i:2405056 original size:25 final size:24
Alignment explanation
Indices: 2404992--2405068 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 24
2404982 ATATTTATTA
*
2404992 TAATTATAA-ATATAATAACTATTAT
1 TAATTATAATATATAATAA--AATAT
2405017 TAA-TATTAAT-TATAATAAAATAT
1 TAATTA-TAATATATAATAAAATAT
2405040 TAATTATAATATAATAATAAAAATAT
1 TAATTATAATAT-ATAAT-AAAATAT
2405066 TAA
1 TAA
2405069 AATCATTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
23 11 0.24
24 5 0.11
25 19 0.42
26 10 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATTATAATATATAATAAAATAT
Found at i:2405391 original size:14 final size:14
Alignment explanation
Indices: 2405337--2405396 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
2405327 ATTTAAATAG
2405337 TTATATAAAA--AT
1 TTATATAAAATTAT
* *
2405349 TTA-ATTAATTTAT
1 TTATATAAAATTAT
*
2405362 TTAATATAAAAATAT
1 TT-ATATAAAATTAT
*
2405377 TTATATATAATTAT
1 TTATATAAAATTAT
2405391 TTATAT
1 TTATAT
2405397 TTATATATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
11 4 0.11
12 3 0.08
13 4 0.11
14 17 0.46
15 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTATATAAAATTAT
Found at i:2405395 original size:10 final size:10
Alignment explanation
Indices: 2405377--2405475 Score: 64
Period size: 10 Copynumber: 10.2 Consensus size: 10
2405367 ATAAAAATAT
2405377 TTATATATAA
1 TTATATATAA
* *
2405387 TTATTTATAT
1 TTATATATAA
2405397 TTATATATAA
1 TTATATATAA
2405407 TTGATA-AT-A
1 TT-ATATATAA
*
2405416 TTTTATATAA
1 TTATATATAA
* * *
2405426 TAACATGTAA
1 TTATATATAA
* *
2405436 ATATA-ATAT
1 TTATATATAA
2405445 TTATATATAA
1 TTATATATAA
2405455 TT-TATA-ATA
1 TTATATATA-A
*
2405464 TTTTATATAA
1 TTATATATAA
2405474 TT
1 TT
2405476 TGTAATGTTT
Statistics
Matches: 66, Mismatches: 16, Indels: 14
0.69 0.17 0.15
Matches are distributed among these distances:
8 3 0.05
9 18 0.27
10 41 0.62
11 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (10 bp):
TTATATATAA
Found at i:2405396 original size:28 final size:25
Alignment explanation
Indices: 2405337--2405396 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 25
2405327 ATTTAAATAG
2405337 TTATATAAAAATTTAATTAATTTAT
1 TTATATAAAAATTTAATTAATTTAT
2405362 TTAATATAAAAATATTTATATATAA-TTAT
1 TT-ATAT-AAAA-ATTTA-AT-TAATTTAT
2405391 TTATAT
1 TTATAT
2405397 TTATATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 2 0.07
26 4 0.13
27 4 0.13
28 9 0.30
29 8 0.27
30 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATATAAAAATTTAATTAATTTAT
Found at i:2405444 original size:68 final size:67
Alignment explanation
Indices: 2405372--2405562 Score: 183
Period size: 68 Copynumber: 2.8 Consensus size: 67
2405362 TTAATATAAA
2405372 AATATTTATATATAATTATTTATATTTATATATAATTGATAATATTTTATATAATAACATGTAAA
1 AATATTTATATATAATTATTTATATTTATATATAATTGATAATATTTTATATAATAACAT-TAAA
2405437 TAT
65 TAT
* * * **
2405440 AATATTTATATATAATT-TATAATATTT-TATATAATTTG-TAATGTTTATATTTAACTATTATT
1 AATATTTATATATAATTAT-TTATATTTATATATAA-TTGATAATATTT-TATATAA-TAACATT
** *
2405502 ATTTGT
62 AAATAT
* * * * *
2405508 AATGTTTATATTTAACTCA-TTATGTTTATATATAATTGATAATATTTTATGTAAT
1 AATATTTATATATAA-TTATTTATATTTATATATAATTGATAATATTTTATATAAT
2405563 TATTGTAAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
67 16 0.16
68 65 0.65
69 19 0.19
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (67 bp):
AATATTTATATATAATTATTTATATTTATATATAATTGATAATATTTTATATAATAACATTAAAT
AT
Found at i:2405472 original size:19 final size:20
Alignment explanation
Indices: 2405372--2405489 Score: 105
Period size: 20 Copynumber: 5.5 Consensus size: 20
2405362 TTAATATAAA
2405372 AATATTTATATATAA-TTATT
1 AATATTTATATATAATTTA-T
* *
2405392 TATATTTATATATAATTGAT
1 AATATTTATATATAATTTAT
2405412 AATATTTTATATAATAACATGTAAATAT
1 AATA-TTTATAT-AT-A-AT-T---TAT
2405440 AATATTTATATATAATTTAT
1 AATATTTATATATAATTTAT
*
2405460 AATATTT-TATATAATTTGT
1 AATATTTATATATAATTTAT
*
2405479 AATGTTTATAT
1 AATATTTATAT
2405490 TTAACTATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
19 17 0.21
20 31 0.38
21 9 0.11
22 2 0.02
23 2 0.02
24 4 0.05
25 2 0.02
26 2 0.02
27 7 0.09
28 6 0.07
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (20 bp):
AATATTTATATATAATTTAT
Found at i:2405507 original size:29 final size:30
Alignment explanation
Indices: 2405473--2405530 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
2405463 ATTTTATATA
2405473 ATTTGTAATGTTTATATTTAACT-ATTATT
1 ATTTGTAATGTTTATATTTAACTCATTATT
2405502 ATTTGTAATGTTTATATTTAACTCATTAT
1 ATTTGTAATGTTTATATTTAACTCATTAT
2405531 GTTTATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (30 bp):
ATTTGTAATGTTTATATTTAACTCATTATT
Found at i:2405584 original size:16 final size:17
Alignment explanation
Indices: 2405563--2405598 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2405553 TTTATGTAAT
2405563 TATTGTAAAAATTA-TA
1 TATTGTAAAAATTATTA
*
2405579 TATTGTAATAATTATTA
1 TATTGTAAAAATTATTA
2405596 TAT
1 TAT
2405599 AAAAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TATTGTAAAAATTATTA
Found at i:2406314 original size:17 final size:17
Alignment explanation
Indices: 2406284--2406329 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
2406274 AATTTTGTGA
2406284 ATTAAAAAAA--TTACT
1 ATTAAAAAAATTTTACT
2406299 ATTAAAAAAATTTTACT
1 ATTAAAAAAATTTTACT
2406316 -TTCAAAATAAATTT
1 ATT-AAAA-AAATTT
2406330 ATTTAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 9 0.33
18 6 0.22
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAAAAAAATTTTACT
Found at i:2410084 original size:32 final size:33
Alignment explanation
Indices: 2410026--2410089 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2410016 TACGAATACA
*
2410026 ATATAAATATATAAATGTATCAAAATTTATATG
1 ATATAAATATATAAATATATCAAAATTTATATG
* *
2410059 ATATAAAT-TATTAATATGTCAAAATTTATAT
1 ATATAAATATATAAATATATCAAAATTTATAT
2410090 AATTTGATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (33 bp):
ATATAAATATATAAATATATCAAAATTTATATG
Found at i:2410211 original size:36 final size:36
Alignment explanation
Indices: 2410164--2410235 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
2410154 ATTATCATAT
2410164 CTATTTGAAATCAAAAGGGCTTCTTAGATGGCAAAC
1 CTATTTGAAATCAAAAGGGCTTCTTAGATGGCAAAC
*
2410200 CTATTTGAAATCAAAAGGGCTTCTTAGATGTCAAAC
1 CTATTTGAAATCAAAAGGGCTTCTTAGATGGCAAAC
2410236 TTGAAATCCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (36 bp):
CTATTTGAAATCAAAAGGGCTTCTTAGATGGCAAAC
Found at i:2410926 original size:115 final size:114
Alignment explanation
Indices: 2410776--2410996 Score: 313
Period size: 119 Copynumber: 1.9 Consensus size: 114
2410766 ACATCTTATA
*
2410776 TTGTACTTTTAAATTTATTATTATTATTAAA-T-TTAATTAATAGTTATATAATGTTTACGTACA
1 TTGTACTTTTAAATTTATTATTATTATTAAATTATTAATTAATAATTATATAATGTTTACGTACA
*
2410839 TAAATAATATTAATTAAT-TGTGCTAATTGACAATTACTTTTAATGGTAATG
66 TAAATAATA-TAATTAATATGT--TAAGTGACAATTACTTTTAATGGTAATG
* * * *
2410890 TTGTCCTTTTGAATTTTTTTATTATTATTAAATTTAATTAATTAATAATTATATTATGTTTACGT
1 TTGTACTTTT-AAATTTATTATTATTATTAAA-TT-ATTAATTAATAATTATATAATGTTTACGT
2410955 ACATAAATAATATAATTAATATGTTAAGTGACAATTACTTTT
63 ACATAAATAATATAATTAATATGTTAAGTGACAATTACTTTT
2410997 GAACTACAGT
Statistics
Matches: 95, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
114 9 0.09
115 19 0.20
117 18 0.19
118 8 0.08
119 41 0.43
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (114 bp):
TTGTACTTTTAAATTTATTATTATTATTAAATTATTAATTAATAATTATATAATGTTTACGTACA
TAAATAATATAATTAATATGTTAAGTGACAATTACTTTTAATGGTAATG
Found at i:2412213 original size:28 final size:28
Alignment explanation
Indices: 2412151--2412214 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
2412141 ATTGTTCATG
*
2412151 TATTTAT-ATTATATTTATAAATTTTAT
1 TATTTATAATTATATTTAAAAATTTTAT
* *
2412178 TAGATTATAATTGTATTTAAAATATTTTA-
1 TA-TTTATAATTATATTTAAAA-ATTTTAT
2412207 TATTTATA
1 TATTTATA
2412215 TAAATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
27 2 0.07
28 9 0.30
29 13 0.43
30 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
TATTTATAATTATATTTAAAAATTTTAT
Found at i:2412235 original size:18 final size:17
Alignment explanation
Indices: 2412201--2412250 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2412191 TATTTAAAAT
2412201 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
2412218 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
2412235 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
2412250 A
1 A
2412251 ATATTGTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.10
14 2 0.07
15 5 0.17
16 3 0.10
17 7 0.24
18 6 0.21
19 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:2413442 original size:2 final size:2
Alignment explanation
Indices: 2413432--2413461 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2413422 TTTTTTCTTT
*
2413432 TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2413462 ATTTTATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:2421085 original size:13 final size:13
Alignment explanation
Indices: 2421064--2421110 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 13
2421054 ATAAAATTTT
*
2421064 ATAAAAATTAAAA
1 ATAATAATTAAAA
2421077 ATAATAATT-AAA
1 ATAATAATTAAAA
2421089 AT-AT--TTAAAA
1 ATAATAATTAAAA
2421099 ATAATAA-TAAAA
1 ATAATAATTAAAA
2421111 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
9 2 0.07
10 5 0.17
11 4 0.14
12 10 0.34
13 8 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATAATTAAAA
Found at i:2421097 original size:22 final size:21
Alignment explanation
Indices: 2421064--2421111 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
2421054 ATAAAATTTT
2421064 ATAAAA-A-TTAAAAATAATA
1 ATAAAATATTTAAAAATAATA
2421083 ATTAAAATATTTAAAAATAATA
1 A-TAAAATATTTAAAAATAATA
2421105 ATAAAAT
1 ATAAAAT
2421112 TAAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.04
20 5 0.19
21 7 0.27
22 13 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAATATTTAAAAATAATA
Found at i:2421101 original size:19 final size:19
Alignment explanation
Indices: 2421067--2421127 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 19
2421057 AAATTTTATA
2421067 AAAATTAAAAATAA-TAATT
1 AAAATTAAAAATAATTAA-T
2421086 AAAATATTTAAAAATAA-TAAT
1 -AAA-A-TTAAAAATAATTAAT
2421107 AAAATTAAAAA-AATTAAT
1 AAAATTAAAAATAATTAAT
2421125 AAA
1 AAA
2421128 TATCTCAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.05
18 14 0.37
19 1 0.03
20 6 0.16
21 2 0.05
22 13 0.34
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATTAAAAATAATTAAT
Found at i:2421119 original size:21 final size:22
Alignment explanation
Indices: 2421073--2421126 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
2421063 TATAAAAATT
**
2421073 AAAAATAATAATTAAAATATTT
1 AAAAATAATAATTAAAATATAA
2421095 AAAAATAATAA-TAAAAT-TAA
1 AAAAATAATAATTAAAATATAA
2421115 AAAAATTAATAA
1 AAAAA-TAATAA
2421127 ATATCTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 12 0.41
22 11 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAATAATAATTAAAATATAA
Found at i:2421128 original size:28 final size:28
Alignment explanation
Indices: 2421065--2421129 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
2421055 TAAAATTTTA
* * *
2421065 TAAAAATTAAAAATAATAATTAAAATATT
1 TAAAAA-TAATAATAATAATTAAAAAAAT
2421094 TAAAAATAATAATAA-AATTAAAAAAAT
1 TAAAAATAATAATAATAATTAAAAAAAT
2421121 TAATAAATA
1 TAA-AAATA
2421130 TCTCAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 13 0.41
28 13 0.41
29 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
TAAAAATAATAATAATAATTAAAAAAAT
Found at i:2424083 original size:12 final size:12
Alignment explanation
Indices: 2424066--2424090 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2424056 TAAACTGTTG
2424066 TTATTAATTAAT
1 TTATTAATTAAT
2424078 TTATTAATTAAT
1 TTATTAATTAAT
2424090 T
1 T
2424091 AAAGTTAATC
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTAATTAAT
Found at i:2430120 original size:14 final size:13
Alignment explanation
Indices: 2430101--2430134 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2430091 TGTTGAGGTG
2430101 ATATATATAT-TT
1 ATATATATATATT
2430113 ATATATATATATT
1 ATATATATATATT
2430126 ATATA-ATAT
1 ATATATATAT
2430135 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATATATATT
Found at i:2436881 original size:36 final size:34
Alignment explanation
Indices: 2436840--2436907 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
2436830 AATCATATCG
* * *
2436840 ATTAAAAATATTATTATTTTTAATATATATTTAATA
1 ATTAAAAAT-TT-TTATATTGAATAAATATTTAATA
2436876 ATTAAAAATTTTTATATTGAATAAATATTTAA
1 ATTAAAAATTTTTATATTGAATAAATATTTAA
2436908 ATATTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 18 0.62
35 2 0.07
36 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (34 bp):
ATTAAAAATTTTTATATTGAATAAATATTTAATA
Found at i:2438145 original size:15 final size:16
Alignment explanation
Indices: 2438061--2438156 Score: 63
Period size: 16 Copynumber: 5.8 Consensus size: 16
2438051 ACATATATGT
*
2438061 ATTAATATAATATTAA
1 ATTAATAAAATATTAA
2438077 CATTAA-AAAACTAAATTAA
1 -ATTAATAAAA-T--ATTAA
* * * *
2438096 ATTATTTATATTTTGAA
1 ATTAATAAAATATT-AA
2438113 ATTTAATAAAATATTAA
1 A-TTAATAAAATATTAA
2438130 ATTAATAAAA-ATTAA
1 ATTAATAAAATATTAA
*
2438145 ATTTA-AAAATAT
1 ATTAATAAAATAT
2438157 ATATATATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
14 4 0.06
15 11 0.18
16 14 0.23
17 12 0.19
18 14 0.23
19 7 0.11
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (16 bp):
ATTAATAAAATATTAA
Found at i:2439533 original size:16 final size:16
Alignment explanation
Indices: 2439509--2439540 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2439499 ATATATTAAA
2439509 AAAACACATAATTTTT
1 AAAACACATAATTTTT
*
2439525 AAAATACATAATTTTT
1 AAAACACATAATTTTT
2439541 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAACACATAATTTTT
Found at i:2459252 original size:2 final size:2
Alignment explanation
Indices: 2459245--2459269 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2459235 CGTGTTTATT
2459245 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
2459270 GCTACCAAAA
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:2460918 original size:389 final size:387
Alignment explanation
Indices: 2460201--2460982 Score: 1546
Period size: 389 Copynumber: 2.0 Consensus size: 387
2460191 CACGGGGAAG
2460201 AACCTGATCCAAAGAACATATCAACACATTTCATCATGCACAAATTACTCTAGAAAAGGTAGATA
1 AACCTGATCCAAAGAACATATCAACACATTTCATCATGCACAAATTACTCTAGAAAAGGTAGATA
2460266 AGGCATAGCGATCCCATAGGATCAGGCATACTTCCATGCAATATAACAGTCAACCAAATTAACTA
66 AGGCATAGCGATCCCATAGGATCAGGCATACTTCCATGCAATATAACAGTCAACCAAATTAACTA
2460331 TGAGAATACTTTAGTTCACAGAGCAGCGTAGTTAAGCAATTAAATTTATTGCTACATCATAGAAT
131 TGAGAATACTTTAGTTCACAGAGCAGCGTAGTTAAGCAATTAAATTTATTGCTACATCATAGAAT
2460396 ATTGTAAAAGAAACTAGGATCAAAATTCTTGACTTTTAAGAATTCTAAATAAAAGACATATACTA
196 ATTGTAAAAGAAACTAGGATCAAAATTCTTGACTTTTAAGAATTCTAAATAAAAGACATATACTA
2460461 AACACGGTATACCTTCTACATATAGTAAATACTGTAGTCCCTTCTAATTGTAATAACTTTGGAAC
261 AACACGGTATACCTTCTACATATAGTAAATACTGTAGTCCCTTCTAATTGTAATAACTTTGGAAC
2460526 AAACCAAATCTCCATCAATGACAAACCCCCCCCCCCCCCCCCCCAAAAAAAAAGTTCACGTGAC
326 AAACCAAATCTCCATCAATGACAAA--CCCCCCCCCCCCCCCCCAAAAAAAAAGTTCACGTGAC
2460590 AACCTGATCCAAAGAACATATCAACACATTTCATCATGCACAAATTACTCTAGAAAAGGTAGATA
1 AACCTGATCCAAAGAACATATCAACACATTTCATCATGCACAAATTACTCTAGAAAAGGTAGATA
2460655 AGGCATAGCGATCCCATAGGATCAGGCATACTTCCATGCAATATAACAGTCAACCAAATTAACTA
66 AGGCATAGCGATCCCATAGGATCAGGCATACTTCCATGCAATATAACAGTCAACCAAATTAACTA
2460720 TGAGAATACTTTAGTTCACAGAGCAGCGTAGTTAAGCAATTAAATTTATTGCTACATCATAGAAT
131 TGAGAATACTTTAGTTCACAGAGCAGCGTAGTTAAGCAATTAAATTTATTGCTACATCATAGAAT
2460785 ATTGTAAAAGAAACTAGGATCAAAATTCTTGACTTTTAAGAATTCTAAATAAAAGACATATACTA
196 ATTGTAAAAGAAACTAGGATCAAAATTCTTGACTTTTAAGAATTCTAAATAAAAGACATATACTA
2460850 AACACGGTATACCTTCTACATATAGTAAATACTGTAGTCCCTTCTAATTGTAATAACTTTGGAAC
261 AACACGGTATACCTTCTACATATAGTAAATACTGTAGTCCCTTCTAATTGTAATAACTTTGGAAC
2460915 AAACCAAATCTCCATCAATGACAAACCCCCCCCCCCCCCCCCAAAAAAAAAGTTCACGTGAC
326 AAACCAAATCTCCATCAATGACAAACCCCCCCCCCCCCCCCCAAAAAAAAAGTTCACGTGAC
2460977 AACCTG
1 AACCTG
2460983 TCAACTAGAT
Statistics
Matches: 393, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
387 43 0.11
389 350 0.89
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (387 bp):
AACCTGATCCAAAGAACATATCAACACATTTCATCATGCACAAATTACTCTAGAAAAGGTAGATA
AGGCATAGCGATCCCATAGGATCAGGCATACTTCCATGCAATATAACAGTCAACCAAATTAACTA
TGAGAATACTTTAGTTCACAGAGCAGCGTAGTTAAGCAATTAAATTTATTGCTACATCATAGAAT
ATTGTAAAAGAAACTAGGATCAAAATTCTTGACTTTTAAGAATTCTAAATAAAAGACATATACTA
AACACGGTATACCTTCTACATATAGTAAATACTGTAGTCCCTTCTAATTGTAATAACTTTGGAAC
AAACCAAATCTCCATCAATGACAAACCCCCCCCCCCCCCCCCAAAAAAAAAGTTCACGTGAC
Found at i:2466842 original size:12 final size:12
Alignment explanation
Indices: 2466825--2466880 Score: 58
Period size: 13 Copynumber: 4.4 Consensus size: 12
2466815 ATTTAAAAAA
2466825 TAAATTTAATTT
1 TAAATTTAATTT
2466837 TAAATTTAATTAT
1 TAAATTTAATT-T
* * *
2466850 TTATTTTTATATT
1 TAAATTTAAT-TT
2466863 TAAATTTAAATTT
1 TAAATTT-AATTT
2466876 TAAAT
1 TAAAT
2466881 AAATTTCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
12 11 0.31
13 21 0.60
14 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TAAATTTAATTT
Found at i:2466857 original size:20 final size:20
Alignment explanation
Indices: 2466828--2466880 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2466818 TAAAAAATAA
2466828 ATTTAATTTTAAATTTAATT
1 ATTTAATTTTAAATTTAATT
* *
2466848 ATTTATTTTTATATTTAA--
1 ATTTAATTTTAAATTTAATT
2466866 ATTTAAATTTTAAAT
1 ATTT-AATTTTAAAT
2466881 AAATTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.14
19 8 0.29
20 16 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTAATTTTAAATTTAATT
Found at i:2466983 original size:19 final size:19
Alignment explanation
Indices: 2466961--2467023 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
2466951 TTTACTTTTC
*
2466961 TTAATTATTTAAATTTAAT
1 TTAATTATTTAAATTAAAT
*
2466980 TTAATAATTATTAAATTAAAT
1 TTAATTA-T-TTAAATTAAAT
* *
2467001 TTAAATT-TTTTAATTCAAT
1 TT-AATTATTTAAATTAAAT
2467020 TTAA
1 TTAA
2467024 ATAATTTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.06
19 17 0.47
20 2 0.06
21 12 0.33
22 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATTATTTAAATTAAAT
Found at i:2467013 original size:41 final size:42
Alignment explanation
Indices: 2466963--2467042 Score: 103
Period size: 41 Copynumber: 1.9 Consensus size: 42
2466953 TACTTTTCTT
*
2466963 AATTATTTAAATTTAATTT-AATAA-TTATTAAAT-TAAATTTA
1 AATTATTT-AATTCAATTTAAATAATTTA-TAAATATAAATTTA
*
2467004 AATTTTTTAATTCAATTTAAATAATTTATAAATATAAAT
1 AATTATTTAATTCAATTTAAATAATTTATAAATATAAAT
2467043 ATTTCATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 9 0.26
41 17 0.50
42 8 0.24
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (42 bp):
AATTATTTAATTCAATTTAAATAATTTATAAATATAAATTTA
Found at i:2467031 original size:19 final size:19
Alignment explanation
Indices: 2466993--2467043 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
2466983 ATAATTATTA
**
2466993 AATTAAATTTAAATTTTTT
1 AATTAAATTTAAATAATTT
*
2467012 AATTCAATTTAAATAATTT
1 AATTAAATTTAAATAATTT
*
2467031 -A-TAAATATAAATA
1 AATTAAATTTAAATA
2467044 TTTCATTTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 10 0.37
18 1 0.04
19 16 0.59
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTAAATTTAAATAATTT
Found at i:2470130 original size:28 final size:28
Alignment explanation
Indices: 2470086--2470139 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
2470076 TGATCAGAAG
2470086 AAAAAAATCGGGATTGGAGTATCCCCTC
1 AAAAAAATCGGGATTGGAGTATCCCCTC
*
2470114 AAAAATAA-CGGGGTTGGAGTATCCCC
1 AAAAA-AATCGGGATTGGAGTATCCCC
2470140 AATTATGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (28 bp):
AAAAAAATCGGGATTGGAGTATCCCCTC
Found at i:2470229 original size:28 final size:28
Alignment explanation
Indices: 2470173--2470249 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
2470163 GGAATAAAGC
*
2470173 CGGGGTTGGAGTATCCGCTCG--GAAGTAA
1 CGGGGTTGGAGTATCC-C-CGATGAAATAA
*
2470201 CGGGGTTGGAATATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
2470229 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
2470250 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 39 0.93
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2470302 original size:52 final size:51
Alignment explanation
Indices: 2470233--2470401 Score: 162
Period size: 52 Copynumber: 3.3 Consensus size: 51
2470223 AAATAACGAG
* * * *
2470233 GTTGGAGTATCCTCGATTGTGAAAAATTGGCATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGC-GTTTTGAAAATAAAACCGGA
** * * *
2470285 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAATACCGGG
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGCGTTTTGAAAATAAAACCGGA
* * ** *
2470337 GTTGGAGTAT-CCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGGG
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGCGTTTTGA-AAATAAAACCGGA
2470388 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
2470402 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
50 1 0.01
51 40 0.42
52 45 0.47
53 10 0.10
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGCGTTTTGAAAATAAAACCGGA
Found at i:2470372 original size:51 final size:51
Alignment explanation
Indices: 2470232--2470400 Score: 166
Period size: 51 Copynumber: 3.3 Consensus size: 51
2470222 GAAATAACGA
* *
2470232 GGTTGGAGTATCCTCGATTGT-GAAAAATTGGCAT-TTTTGGAAATAAAATCGG
1 GGTTGGAGTATCC-CGATTGTGGAAAAATTGG--TGTTTTGAAAATAAAACCGG
* ** * *
2470284 AGTTGGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAATACCGG
1 GGTTGGAGTAT-CCCGATT-GTGGAAAAATTGGTGTTTTGAAAATAAAACCGG
* **
2470336 GGTTGGAGTATCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGG
1 GGTTGGAGTATCCCGATTGTGGAAAAATTGGTGTTTTGA-AAATAAAACCGG
2470387 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
2470401 CTCAGAAATA
Statistics
Matches: 96, Mismatches: 15, Indels: 13
0.77 0.12 0.10
Matches are distributed among these distances:
50 3 0.03
51 42 0.44
52 40 0.42
53 10 0.10
54 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCGATTGTGGAAAAATTGGTGTTTTGAAAATAAAACCGG
Found at i:2470421 original size:211 final size:211
Alignment explanation
Indices: 2470117--2470570 Score: 596
Period size: 211 Copynumber: 2.2 Consensus size: 211
2470107 TCCCCTCAAA
* * * *
2470117 AATAACGGGGTTGGAGTATCCCCAATTAT-GAGAAATTAATATTTTGGGAATAAAGCCGGGGTTG
1 AATAACGGGGTTGGAGTATCCCCGATTATGGAAAAATTAATATTTTGCGAATAAAACCGGGGTTG
* * * * *
2470181 GAGTATCCGCTCGGAAGTAACGGGGTTGGAATATCCCCGATGAAATAACGAGGTTGGAGTATCCT
66 GAGTATCCCCTCAGAAATAACGAGGTTGGAATATCCCCGATG-AATAACGAGGTTGGAGTATCCC
* *
2470246 CGATTGTGAA-AAATTG-GCATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGA
130 CGATTGTGAAGAAATTGAG-ATTTTTGGAAATAAAATCAGAGTTAGAGTATCCCCGATTAAA-GA
*
2470309 AAATTGGCGTTTTGAAAAT
193 AAATTAGCGTTTTGAAAAT
* * * *
2470328 AATACCGGGGTTGGAGTAT-CCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGGGTT
1 AATAACGGGGTTGGAGTATCCCCGATTATGGAAAAATTAATATTTT-GCGAATAAAACCGGGGTT
* * *
2470391 GGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCC
65 GGAGTATCCCCTCAGAAATAACGAGGTTGGAATATCCCCGATGAATAACGAGGTTGGAGTATCCC
* *
2470456 CGATTGTGAAGAAATTGATGTTTTTTGGAAATAAAATCAGAGTTAGAGTATCCCCGATTATAGAA
130 CGATTGTGAAGAAATTGA-GATTTTTGGAAATAAAATCAGAGTTAGAGTATCCCCGATTAAAGAA
*
2470521 AATTAGTGTTTTGAAAAT
194 AATTAGCGTTTTGAAAAT
* *
2470539 AA-AATCGGAGTTGGAATATCCCCGATTATGGA
1 AATAA-CGGGGTTGGAGTATCCCCGATTATGGA
2470571 GAATTGAGAA
Statistics
Matches: 210, Mismatches: 26, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
210 37 0.18
211 121 0.58
212 51 0.24
213 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (211 bp):
AATAACGGGGTTGGAGTATCCCCGATTATGGAAAAATTAATATTTTGCGAATAAAACCGGGGTTG
GAGTATCCCCTCAGAAATAACGAGGTTGGAATATCCCCGATGAATAACGAGGTTGGAGTATCCCC
GATTGTGAAGAAATTGAGATTTTTGGAAATAAAATCAGAGTTAGAGTATCCCCGATTAAAGAAAA
TTAGCGTTTTGAAAAT
Found at i:2470447 original size:27 final size:28
Alignment explanation
Indices: 2470384--2470459 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2470374 GCGATAAAAC
*
2470384 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
* *
2470412 CGAGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
2470439 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2470460 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2470478 original size:107 final size:104
Alignment explanation
Indices: 2470099--2470479 Score: 290
Period size: 107 Copynumber: 3.6 Consensus size: 104
2470089 AAAATCGGGA
* ** * * * * * *
2470099 TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATTAATATTTTGG
1 TTGGAGTATCCCC-GATGAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGA
* * * *
2470164 GAATAAAGCCGGGGTTGGAGTATCCGCTCGGAAGTAACGGGG
65 G-ATAAAACCGGGGTTGGAGTATCCCCTC-GAAATAACGAGG
* * *
2470206 TTGGAATATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGCAT-TTTT
1 TTGGAGTATCCCCGATG-AATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATT-G-ATGTTTT
* * * * * **
2470270 GGAAATAAAATCGGAGTTGGAGTAT-CCC-CG-ATTAAAGGAAAA
63 -GAGATAAAACCGGGGTTGGAGTATCCCCTCGAAAT-AACG-AGG
* * ***** *
2470312 TTGGCGTTTTGAAAAT-AATACCGGGGTTGGAGTAT-CCCGATTGTGGAAAAATT-AGTGTTTTA
1 TTGGAGTATCCCCGATGAATAACGGGGTTGGAGTATCCCCGATTGT-GAAAAATTGA-TGTTTT-
*
2470374 GCGATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGAGG
63 GAGATAAAACCGGGGTTGGAGTATCCCCTC-GAAATAACGAGG
*
2470417 TTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGATGTTTT
1 TTGGAGTATCCCCGATGAATAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTGATGTTTT
2470480 TTGGAAATAA
Statistics
Matches: 207, Mismatches: 50, Indels: 34
0.71 0.17 0.12
Matches are distributed among these distances:
101 1 0.00
102 1 0.00
103 32 0.15
104 30 0.14
105 15 0.07
106 34 0.16
107 68 0.33
108 23 0.11
109 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (104 bp):
TTGGAGTATCCCCGATGAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAG
ATAAAACCGGGGTTGGAGTATCCCCTCGAAATAACGAGG
Found at i:2470543 original size:51 final size:54
Alignment explanation
Indices: 2470447--2470577 Score: 155
Period size: 51 Copynumber: 2.5 Consensus size: 54
2470437 AACGGGGTTG
* * *
2470447 GAGTATCCCCGATTGTGAAGAAATTGATGTTTTTTGGAAATAAAATCAGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTGATGTGTTTTGAAAATAAAATCAGAGTTA
* *
2470501 GAGTATCCCCGATTAT--AGAAAATT-A-GTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTGATGTGTTTTGAAAATAAAATCAGAGTTA
* *
2470552 GAATATCCCCGATTATGGAG-AATTGA
1 GAGTATCCCCGATTATGAAGAAATTGA
2470578 GAAACTCGAC
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
51 41 0.61
52 4 0.06
53 7 0.10
54 15 0.22
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (54 bp):
GAGTATCCCCGATTATGAAGAAATTGATGTGTTTTGAAAATAAAATCAGAGTTA
Found at i:2472388 original size:11 final size:11
Alignment explanation
Indices: 2472372--2472403 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
2472362 TAATGGAATA
2472372 GTGTTTTTTTT
1 GTGTTTTTTTT
2472383 GTG-TTTTTTT
1 GTGTTTTTTTT
2472393 G-GTTTTTTTT
1 GTGTTTTTTTT
2472403 G
1 G
2472404 CTAAAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.05
10 16 0.80
11 3 0.15
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (11 bp):
GTGTTTTTTTT
Found at i:2472951 original size:33 final size:33
Alignment explanation
Indices: 2472913--2472979 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2472903 AAAATTTCCA
* ***
2472913 AATGTATTGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2472946 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2472979 A
1 A
2472980 TTTCCTTGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2472952 original size:13 final size:13
Alignment explanation
Indices: 2472934--2472959 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2472924 ACAAAGATCC
2472934 ATGTATCGATACA
1 ATGTATCGATACA
2472947 ATGTATCGATACA
1 ATGTATCGATACA
2472960 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2473023 original size:19 final size:18
Alignment explanation
Indices: 2472999--2473066 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
2472989 TAGTAGCTAA
2472999 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
*
2473018 TTATGTATTGATAC--A-
1 TTATGTATCGATACAAAC
2473033 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2473050 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2473067 TTGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2473043 original size:32 final size:32
Alignment explanation
Indices: 2473002--2473064 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2472992 TAGCTAATTA
* *
2473002 TGTATCGATACAATACTTATGTATTGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2473034 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2473065 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2473598 original size:20 final size:19
Alignment explanation
Indices: 2473553--2473603 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2473543 TTTAAAGTTA
* *
2473553 ATTAATATGATATTTATGC
1 ATTAATATTATATTAATGC
2473572 ATGTAATATTATATTAAATGC
1 AT-TAATATTATATT-AATGC
2473593 ATTAAT-TTATA
1 ATTAATATTATA
2473604 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.25
20 15 0.54
21 6 0.21
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (19 bp):
ATTAATATTATATTAATGC
Found at i:2474347 original size:12 final size:11
Alignment explanation
Indices: 2474311--2474346 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2474301 ACTTTGTAAA
2474311 TTATTCTAATTT
1 TTATT-TAATTT
2474323 TTATTTAATTT
1 TTATTTAATTT
*
2474334 TTATTTTATTT
1 TTATTTAATTT
2474345 TT
1 TT
2474347 TTAAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTAATTT
Found at i:2474537 original size:23 final size:23
Alignment explanation
Indices: 2474511--2474556 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2474501 TTTTTTTTAA
* *
2474511 TATTTTAAA-AAATATATAATTAT
1 TATTATAAATAAAAATA-AATTAT
2474534 TATTATAAATAAAAATAAATTAT
1 TATTATAAATAAAAATAAATTAT
2474557 GTTATCACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTATAAATAAAAATAAATTAT
Found at i:2474905 original size:20 final size:20
Alignment explanation
Indices: 2474882--2474927 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2474872 TAATATATAT
*
2474882 TTTTATTTAAAAAATTAATA
1 TTTTAATTAAAAAATTAATA
* **
2474902 TTTTAATTAATATTTTAATA
1 TTTTAATTAAAAAATTAATA
2474922 TTTTAA
1 TTTTAA
2474928 AATAATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAATTAAAAAATTAATA
Found at i:2474911 original size:12 final size:12
Alignment explanation
Indices: 2474894--2474920 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2474884 TTATTTAAAA
2474894 AATTAATATTTT
1 AATTAATATTTT
2474906 AATTAATATTTT
1 AATTAATATTTT
2474918 AAT
1 AAT
2474921 ATTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATTAATATTTT
Found at i:2476134 original size:59 final size:58
Alignment explanation
Indices: 2476062--2476190 Score: 240
Period size: 59 Copynumber: 2.2 Consensus size: 58
2476052 TATAAGTTAC
2476062 ATTTATTAAATTTATTTGTAAATTAAATGAGATCACGTCAATCAAAAATATTAAATTAT
1 ATTTATTAAATTTATTTGTAAATTAAATGAGATCAC-TCAATCAAAAATATTAAATTAT
*
2476121 ATTTATTAAATTTATTTGTAAATTAAATGAGATCACTTAATCAAAAATATTAAATTAT
1 ATTTATTAAATTTATTTGTAAATTAAATGAGATCACTCAATCAAAAATATTAAATTAT
2476179 ATTTATTAAATT
1 ATTTATTAAATT
2476191 AAATAAATAA
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
58 33 0.48
59 36 0.52
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (58 bp):
ATTTATTAAATTTATTTGTAAATTAAATGAGATCACTCAATCAAAAATATTAAATTAT
Found at i:2476676 original size:22 final size:21
Alignment explanation
Indices: 2476625--2476679 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2476615 AAATTATTTT
2476625 AAATTTAAATTTAATTATAAA
1 AAATTTAAATTTAATTATAAA
* *
2476646 ATATATAAATATTAATT-TAAA
1 AAATTTAAAT-TTAATTATAAA
2476667 ACAATTTAAATTT
1 A-AATTTAAATTT
2476680 TGAATGAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTTAAATTTAATTATAAA
Found at i:2477360 original size:31 final size:32
Alignment explanation
Indices: 2477316--2477379 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
2477306 TATATCAATA
2477316 ATTATATTTTTAATTAAAT-TTAAATAAAATT
1 ATTATATTTTTAATTAAATATTAAATAAAATT
* *
2477347 ATTAT-TTTATTAATTAAATATTAATTCAAATT
1 ATTATATTT-TTAATTAAATATTAAATAAAATT
2477379 A
1 A
2477380 AATTTAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 3 0.10
31 15 0.52
32 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTATATTTTTAATTAAATATTAAATAAAATT
Found at i:2477875 original size:11 final size:11
Alignment explanation
Indices: 2477859--2477984 Score: 53
Period size: 10 Copynumber: 12.1 Consensus size: 11
2477849 TTATTAATTT
2477859 TAAATATAATA
1 TAAATATAATA
2477870 TAAATATATTATTA
1 TAAATATA--A-TA
*
2477884 TAAAAATAAT-
1 TAAATATAATA
2477894 TAAA-AT-ATGA
1 TAAATATAAT-A
2477904 T-AA-A-AATA
1 TAAATATAATA
2477912 TAAATATAATA
1 TAAATATAATA
2477923 -AAA-AT-ATA
1 TAAATATAATA
*
2477931 TAAATATATTA
1 TAAATATAATA
*
2477942 -AAAT-TTATA
1 TAAATATAATA
2477951 TAAA-ATTAATTA
1 TAAATA-TAA-TA
*
2477963 TTAATAT-ATA
1 TAAATATAATA
* *
2477973 AAAATAAAATA
1 TAAATATAATA
2477984 T
1 T
2477985 TTTAAATATA
Statistics
Matches: 87, Mismatches: 10, Indels: 36
0.65 0.08 0.27
Matches are distributed among these distances:
8 7 0.08
9 17 0.20
10 24 0.28
11 21 0.24
12 7 0.08
13 2 0.02
14 9 0.10
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (11 bp):
TAAATATAATA
Done.