Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001871.1 Hibiscus syriacus cultivar Beakdansim tig00003793_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 159962
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:10749 original size:7 final size:7
Alignment explanation
Indices: 10732--10781 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
10722 CCCCATTTTG
10732 CTCTATCT
1 CTCT-TCT
10740 CTCTTCT
1 CTCTTCT
10747 CTCTTCT
1 CTCTTCT
*
10754 TTCTTCT
1 CTCTTCT
*
10761 TTCTTCT
1 CTCTTCT
*
10768 CCCTTCT
1 CTCTTCT
*
10775 CCCTTCT
1 CTCTTCT
10782 TTTTTTTTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
7 35 0.90
8 4 0.10
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (7 bp):
CTCTTCT
Found at i:13769 original size:17 final size:17
Alignment explanation
Indices: 13749--13841 Score: 54
Period size: 17 Copynumber: 5.4 Consensus size: 17
13739 ATAGAAATGT
13749 TTAAATTATAGTAGAAA
1 TTAAATTATAGTAGAAA
*
13766 TTAAATCCATA--A-AAA
1 TTAAAT-TATAGTAGAAA
13781 TGTTTAAATTATAGTAGAAA
1 ---TTAAATTATAGTAGAAA
*
13801 TTAAATCCATA--A-AAA
1 TTAAAT-TATAGTAGAAA
13816 TGTTTAAATTATAGTAGAAA
1 ---TTAAATTATAGTAGAAA
13836 TTAAAT
1 TTAAAT
13842 CCATAAACAA
Statistics
Matches: 58, Mismatches: 4, Indels: 28
0.64 0.04 0.31
Matches are distributed among these distances:
15 6 0.10
16 2 0.03
17 24 0.41
18 18 0.31
19 2 0.03
20 6 0.10
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (17 bp):
TTAAATTATAGTAGAAA
Found at i:13782 original size:35 final size:35
Alignment explanation
Indices: 13743--13848 Score: 212
Period size: 35 Copynumber: 3.0 Consensus size: 35
13733 ACATAGATAG
13743 AAATGTTTAAATTATAGTAGAAATTAAATCCATAA
1 AAATGTTTAAATTATAGTAGAAATTAAATCCATAA
13778 AAATGTTTAAATTATAGTAGAAATTAAATCCATAA
1 AAATGTTTAAATTATAGTAGAAATTAAATCCATAA
13813 AAATGTTTAAATTATAGTAGAAATTAAATCCATAA
1 AAATGTTTAAATTATAGTAGAAATTAAATCCATAA
13848 A
1 A
13849 CAACAGGGAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 71 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (35 bp):
AAATGTTTAAATTATAGTAGAAATTAAATCCATAA
Found at i:13789 original size:18 final size:18
Alignment explanation
Indices: 13766--13824 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
13756 ATAGTAGAAA
13766 TTAAATCCATAAAAATGT
1 TTAAATCCATAAAAATGT
*
13784 TTAAAT-TATAGTAGAAA---
1 TTAAATCCATA--A-AAATGT
13801 TTAAATCCATAAAAATGT
1 TTAAATCCATAAAAATGT
13819 TTAAAT
1 TTAAAT
13825 TATAGTAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 3 0.09
16 1 0.03
17 9 0.28
18 15 0.47
19 1 0.03
20 3 0.09
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (18 bp):
TTAAATCCATAAAAATGT
Found at i:16879 original size:2 final size:2
Alignment explanation
Indices: 16872--16900 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16862 TTAAACATAA
16872 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16901 AAAGAAATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17497 original size:24 final size:24
Alignment explanation
Indices: 17470--17549 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
17460 CGTTCATTTA
**
17470 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCGTGTTCGTTCGGTTATGTT
17494 CGTTCGGTTATGTTCGTTCGGTTATGTT
1 CGTTC-G---TGTTCGTTCGGTTATGTT
**
17522 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCGTGTTCGTTCGGTTATGTT
17546 CGTT
1 CGTT
17550 TATGTTCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 27 0.56
25 1 0.02
28 20 0.42
ACGTcount: A:0.09, C:0.15, G:0.28, T:0.49
Consensus pattern (24 bp):
CGTTCGTGTTCGTTCGGTTATGTT
Found at i:17499 original size:14 final size:14
Alignment explanation
Indices: 17480--17549 Score: 112
Period size: 14 Copynumber: 5.3 Consensus size: 14
17470 CGTTCGTGAA
17480 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
17494 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
17508 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
17522 CG-T---TTATGTT
1 CGTTCGGTTATGTT
17532 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
17546 CGTT
1 CGTT
17550 TATGTTCATT
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.17
11 1 0.02
13 1 0.02
14 41 0.79
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:17512 original size:38 final size:38
Alignment explanation
Indices: 17470--17549 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
17460 CGTTCATTTA
17470 CGTTC-GTGAACGTTCGGTTATGTTCGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTTCGTTCGGTTATGTT
* * *
17508 CGTTCGGTTATGTTCGTTTATGTTCGTTCGGTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTTCGTTCGGTTATGTT
17546 CGTT
1 CGTT
17550 TATGTTCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 36 0.95
39 2 0.05
ACGTcount: A:0.09, C:0.15, G:0.28, T:0.49
Consensus pattern (38 bp):
CGTTCGGTAACGTTCGGTTATGTTCGTTCGGTTATGTT
Found at i:17566 original size:38 final size:37
Alignment explanation
Indices: 17487--17569 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 37
17477 GAACGTTCGG
* *
17487 TTATGTTCGTTCGGTTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGTTAGGTTA-GTTCAT
*
17525 TTATGTTCGTTCGGTTATGTTCGTTTATGTTCA-TTCAT
1 TTATGTTCGTTCGGTTATGTTCG-TTAGGTT-AGTTCAT
17563 TTATGTT
1 TTATGTT
17570 TAACCCAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
38 34 0.85
39 5 0.12
40 1 0.03
ACGTcount: A:0.11, C:0.12, G:0.22, T:0.55
Consensus pattern (37 bp):
TTATGTTCGTTCGGTTATGTTCGTTAGGTTAGTTCAT
Found at i:17569 original size:24 final size:24
Alignment explanation
Indices: 17480--17556 Score: 118
Period size: 24 Copynumber: 3.0 Consensus size: 24
17470 CGTTCGTGAA
17480 CGTTCGGTTATGTTCGTTCGGTTATGTT
1 CGTTCGGTTATGTTCG-T---TTATGTT
17508 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
17532 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
17556 C
1 C
17557 ATTCATTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 32 0.65
27 1 0.02
28 16 0.33
ACGTcount: A:0.08, C:0.14, G:0.26, T:0.52
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:18649 original size:16 final size:16
Alignment explanation
Indices: 18628--18694 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
18618 GTCTCCAACG
18628 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
18644 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
** *
18660 TTTATGTTCGTGCGCG
1 TTTATGTTCGTGTTCA
18676 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
18690 TTTAT
1 TTTAT
18695 TAAATGAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 5 0.11
16 40 0.89
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.57
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:18667 original size:32 final size:32
Alignment explanation
Indices: 18626--18686 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
18616 GGGTCTCCAA
**
18626 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGCGCATTTATGTTCGTGTT
*
18658 CGTTTATGTTCGTGCGCGTTTATGTTCGT
1 CGTTTATGTTCGTGCGCATTTATGTTCGT
18687 TTATTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.08, C:0.15, G:0.25, T:0.52
Consensus pattern (32 bp):
CGTTTATGTTCGTGCGCATTTATGTTCGTGTT
Found at i:22545 original size:15 final size:15
Alignment explanation
Indices: 22507--22578 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 15
22497 GGAAAATTAG
*
22507 GAAAATGAATTA-TT
1 GAAAATGAATTACTA
*
22521 GAAATTTGAATTACTA
1 GAAA-ATGAATTACTA
*
22537 GAAAATGAATTACTG
1 GAAAATGAATTACTA
** *
22552 GAATTTAAATT-CTA
1 GAAAATGAATTACTA
22566 GAAAATGAATTAC
1 GAAAATGAATTAC
22579 ATTTATGGAA
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
14 14 0.32
15 25 0.57
16 5 0.11
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (15 bp):
GAAAATGAATTACTA
Found at i:22576 original size:29 final size:30
Alignment explanation
Indices: 22507--22578 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
22497 GGAAAATTAG
* *
22507 GAAAATGAATTATTGAAATTTGAATTACTA
1 GAAAATGAATTACTGAAATTTAAATTACTA
*
22537 GAAAATGAATTACTGGAATTTAAATT-CTA
1 GAAAATGAATTACTGAAATTTAAATTACTA
22566 GAAAATGAATTAC
1 GAAAATGAATTAC
22579 ATTTATGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (30 bp):
GAAAATGAATTACTGAAATTTAAATTACTA
Found at i:22923 original size:23 final size:23
Alignment explanation
Indices: 22890--22934 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
22880 AGTGTTATAT
*
22890 TATATTTTAAAAATATTAATTAG
1 TATATTGTAAAAATATTAATTAG
* *
22913 TATATTGTAAATATATTTATTA
1 TATATTGTAAAAATATTAATTA
22935 AAATATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TATATTGTAAAAATATTAATTAG
Found at i:22940 original size:23 final size:23
Alignment explanation
Indices: 22891--22941 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
22881 GTGTTATATT
* **
22891 ATATTTTAAAAATATTAATTAGT
1 ATATTGTAAAAATATTAATTAAA
* *
22914 ATATTGTAAATATATTTATTAAA
1 ATATTGTAAAAATATTAATTAAA
22937 ATATT
1 ATATT
22942 ATTTAAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
ATATTGTAAAAATATTAATTAAA
Found at i:22981 original size:19 final size:20
Alignment explanation
Indices: 22929--23003 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
22919 GTAAATATAT
22929 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
22948 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
* **
22969 TTATTAAATATATAATTTTT
1 TTATTAAATATATTATTTAA
22989 TTATT--ATATATTATT
1 TTATTAAATATATTATT
23004 AAAATAACAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
18 9 0.20
19 8 0.18
20 16 0.36
21 6 0.13
22 6 0.13
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:23000 original size:59 final size:59
Alignment explanation
Indices: 22928--23086 Score: 150
Period size: 59 Copynumber: 2.7 Consensus size: 59
22918 TGTAAATATA
*
22928 TTTATTAAAATATTATTTAAATATATAA-ATAATATTATTCATTATTAAATATATAATT-TT
1 TTTATT-ATATATTATTTAAATATATAATATAATATTATT-ATTATTAAA-ATATAATTATT
* * *
22988 TTTATTATATATTATTAAAATA-ACAATATAATATCT-TATATTATTATAATATAATTGATT
1 TTTATTATATATTATTTAAATATATAATATAATAT-TAT-TATTATTAAAATATAATT-ATT
* * * *
23048 ATT-TTATATAATA-TTAAAAATATAATATTATATTATTAT
1 TTTATTATATATTATTTAAATATATAATATAATATTATTAT
23087 AAATATTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
58 20 0.24
59 50 0.61
60 12 0.15
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (59 bp):
TTTATTATATATTATTTAAATATATAATATAATATTATTATTATTAAAATATAATTATT
Found at i:23079 original size:22 final size:23
Alignment explanation
Indices: 23054--23097 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
23044 GATTATTTTA
23054 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
23076 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
23098 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:23105 original size:31 final size:31
Alignment explanation
Indices: 22970--23105 Score: 92
Period size: 31 Copynumber: 4.5 Consensus size: 31
22960 TATTATTCAT
* * *
22970 TATTAAATATATAAT-TT-TTTTATTATATAT
1 TATTAAAAATATAATATTATATT-TTATATAA
* * *
23000 TATT-AAAATAACAATATAATATCTTATAT--
1 TATTAAAAAT-ATAATATTATATTTTATATAA
* *
23029 TATT-ATAATATAAT-TGATTATTTTATATAA
1 TATTAAAAATATAATATTA-TATTTTATATAA
23059 TATTAAAAATATAATATTATATTATTATA-AA
1 TATTAAAAATATAATATTATATT-TTATATAA
23090 TATTAATAAAT-TAATA
1 TATTAA-AAATATAATA
23106 AATAATATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 19
0.74 0.10 0.17
Matches are distributed among these distances:
27 2 0.02
28 13 0.15
29 12 0.14
30 12 0.14
31 33 0.39
32 13 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
TATTAAAAATATAATATTATATTTTATATAA
Found at i:23111 original size:52 final size:52
Alignment explanation
Indices: 23012--23114 Score: 120
Period size: 52 Copynumber: 1.9 Consensus size: 52
23002 TTAAAATAAC
** * *
23012 AATATAATATCTTATATTATTATAATATAATTGATTATTTTATATAATATTAAA
1 AATATAATA-CTTATATTATTATAATATAATAAATTA-TATAAATAATATTAAA
23066 AATATAATA-TTATATTATTATAAATATTAATAAATTA-ATAAATAATATT
1 AATATAATACTTATATTATTAT-AATA-TAATAAATTATATAAATAATATT
23115 TTGATGAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
52 22 0.51
53 4 0.09
54 17 0.40
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (52 bp):
AATATAATACTTATATTATTATAATATAATAAATTATATAAATAATATTAAA
Found at i:23383 original size:29 final size:29
Alignment explanation
Indices: 23321--23376 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
23311 ACAAACACTT
23321 GGAAAACATTTTCCGAAAAACGAATTACG
1 GGAAAACATTTTCCGAAAAACGAATTACG
*
23350 GGAAAACATTTTTCGAAAAACGAATTA
1 GGAAAACATTTTCCGAAAAACGAATTA
23377 TGTGAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.23
Consensus pattern (29 bp):
GGAAAACATTTTCCGAAAAACGAATTACG
Found at i:23832 original size:21 final size:21
Alignment explanation
Indices: 23807--23847 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23797 CAACAACTTA
23807 TTTTC-AAAAAAAAATGAGAAT
1 TTTTCTAAAAAAAAA-GAGAAT
*
23828 TTTTCTAAAAAATAAGAGAA
1 TTTTCTAAAAAAAAAGAGAA
23848 AAGTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (21 bp):
TTTTCTAAAAAAAAAGAGAAT
Found at i:26823 original size:24 final size:24
Alignment explanation
Indices: 26774--26826 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
26764 GTTAAAATGA
**
26774 TAAACGAACACAAATGAACTAACG
1 TAAACGAACACAAACAAACTAACG
26798 TAAACGAACACAAACAAAC-AAGCG
1 TAAACGAACACAAACAAACTAA-CG
26822 TAAAC
1 TAAAC
26827 AAATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (24 bp):
TAAACGAACACAAACAAACTAACG
Found at i:27030 original size:10 final size:10
Alignment explanation
Indices: 27017--27050 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
27007 ATAAATGAAC
27017 GAACATAAAT
1 GAACATAAAT
27027 GAACATAAACT
1 GAACATAAA-T
27038 -AACATAAAT
1 GAACATAAAT
27047 GAAC
1 GAAC
27051 GTACATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.59, C:0.15, G:0.09, T:0.18
Consensus pattern (10 bp):
GAACATAAAT
Found at i:46852 original size:60 final size:60
Alignment explanation
Indices: 46704--46881 Score: 191
Period size: 60 Copynumber: 3.0 Consensus size: 60
46694 TACACTACAT
* * * *
46704 ATCCTCAAAGTATGACTCTCATTTTAAGTTGGT-CTCTAAACTTTTAAATATTTCAATTCT
1 ATCCTCAAACTATGACTCTCATTTTAAATTGGTCCTC-AAACATTTAAATATTTCAATTCC
* * * *
46764 ATCC-CTAAACTATGACTATCATTTTAAATTAGTCCTCAAACATTTGAATATTTTAATTCC
1 ATCCTC-AAACTATGACTCTCATTTTAAATTGGTCCTCAAACATTTAAATATTTCAATTCC
* * * *
46824 ATCCTCAAACTATGAC-CTCAATTCTAAATTGGTCCCCAAACTTTCTAAATATTCCAAT
1 ATCCTCAAACTATGACTCTC-ATTTTAAATTGGTCCTCAAACATT-TAAATATTTCAAT
46882 ATCATCCCTT
Statistics
Matches: 97, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
59 3 0.03
60 80 0.82
61 14 0.14
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (60 bp):
ATCCTCAAACTATGACTCTCATTTTAAATTGGTCCTCAAACATTTAAATATTTCAATTCC
Found at i:48200 original size:19 final size:20
Alignment explanation
Indices: 48176--48214 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
48166 TAGATTGTGA
*
48176 ATAAAATATAAA-TCCATTT
1 ATAAAATAGAAATTCCATTT
48195 ATAAAATAGAAATTCCATTT
1 ATAAAATAGAAATTCCATTT
48215 TTTCGAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (20 bp):
ATAAAATAGAAATTCCATTT
Found at i:50727 original size:12 final size:14
Alignment explanation
Indices: 50706--50737 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
50696 TTTTCACTTC
50706 CTTCTCTCTCATTT
1 CTTCTCTCTCATTT
50720 CTTCTCTCTCATTT
1 CTTCTCTCTCATTT
50734 CTTC
1 CTTC
50738 CGTATCTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (14 bp):
CTTCTCTCTCATTT
Found at i:52532 original size:34 final size:35
Alignment explanation
Indices: 52479--52548 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
52469 AAGAAATAAG
*
52479 TTTATGGGCCCTGCTTTTAATTTAGTTTATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
*
52514 TTTATGGG-CTTGCTTTTAATTTAGTATATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
52548 T
1 T
52549 ATTTTTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 25 0.76
35 8 0.24
ACGTcount: A:0.24, C:0.09, G:0.14, T:0.53
Consensus pattern (35 bp):
TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
Found at i:54222 original size:2 final size:2
Alignment explanation
Indices: 54215--54280 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
54205 CAGTTAAAAT
54215 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
54257 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
54281 AATTTCATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54459 original size:33 final size:33
Alignment explanation
Indices: 54411--54477 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
54401 AATAAGACTC
54411 ATAGAAAGATAATTTTCAACGATGAACAAATGA
1 ATAGAAAGATAATTTTCAACGATGAACAAATGA
54444 ATAGAAAGACT-ATTTTCAACGATGAACAAATGA
1 ATAGAAAGA-TAATTTTCAACGATGAACAAATGA
54477 A
1 A
54478 AAATCTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (33 bp):
ATAGAAAGATAATTTTCAACGATGAACAAATGA
Found at i:62707 original size:2 final size:2
Alignment explanation
Indices: 62700--62799 Score: 200
Period size: 2 Copynumber: 50.0 Consensus size: 2
62690 CCCTCACATC
62700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62784 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
62800 GATTTGTATT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65287 original size:19 final size:20
Alignment explanation
Indices: 65263--65301 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
65253 AGGCTGAAAA
65263 TTTAAAAATTAT-TATATAT
1 TTTAAAAATTATATATATAT
65282 TTTAAAAATTATATATATAT
1 TTTAAAAATTATATATATAT
65302 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAAATTATATATATAT
Found at i:65296 original size:2 final size:2
Alignment explanation
Indices: 65291--65353 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
65281 TTTTAAAAAT
65291 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
65333 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
65354 GTAACATCCG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66538 original size:20 final size:22
Alignment explanation
Indices: 66498--66554 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
66488 TGAATGTGTG
*
66498 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
66520 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
66540 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
66555 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:67122 original size:31 final size:31
Alignment explanation
Indices: 67084--67239 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
67074 AGGGTCGAGG
67084 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
67115 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
67146 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
67177 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
67208 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
67239 G
1 G
67240 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:68736 original size:2 final size:2
Alignment explanation
Indices: 68729--68754 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
68719 ATTCATTACA
68729 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
68755 TATCAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69886 original size:92 final size:89
Alignment explanation
Indices: 69709--69928 Score: 237
Period size: 92 Copynumber: 2.4 Consensus size: 89
69699 TTGACCCCTA
* * **
69709 TTTTT-TGAAGTATTTTGGCCCTAACATTTCATTTTAGGTTAAAAAATTCCCTAATGTTTGATCA
1 TTTTTCTGGAGTATTTTGGCCCTAACGTTTCATTTTAGGCAAAAAAATTCCCTAATGTTTGATCA
* * *
69773 AATAATCATTTTAATCTTTATTCTTTT
66 AATAATCACTTTAACCCTTATTC---T
* *
69800 TTTTTCTGGAGTATTTTTGCCCTAACGTTTCATTTTCGAGCAAAAAAATT-CCTAATGTTTGATC
1 TTTTTCTGGAGTATTTTGGCCCTAACGTTTCATTTTAG-GCAAAAAAATTCCCTAATGTTTGATC
* * **
69864 ATATATTCACTTTGGCCCTTATTCT
65 AAATAATCACTTTAACCCTTATTCT
* * *
69889 TATTTCTGGAGCATTTTGGCCTTCAACGTTTCATTTTAGG
1 TTTTTCTGGAGTATTTTGGCCCT-AACGTTTCATTTTAGG
69929 AGAAAATCCT
Statistics
Matches: 108, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
89 21 0.19
90 14 0.13
91 5 0.05
92 59 0.55
93 9 0.08
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (89 bp):
TTTTTCTGGAGTATTTTGGCCCTAACGTTTCATTTTAGGCAAAAAAATTCCCTAATGTTTGATCA
AATAATCACTTTAACCCTTATTCT
Found at i:71615 original size:112 final size:112
Alignment explanation
Indices: 71262--71942 Score: 1118
Period size: 112 Copynumber: 6.1 Consensus size: 112
71252 TCGGTTTGTA
* ** *
71262 TCGATACTTTATAAAAATATATTAATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
*
71327 CTATAAATGACAAAAGAGGTAAAGCGCTACCGGATATATTGAAAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
* * * *
71374 TCGATACTTTATAAAAATATATCGATCTATAACAATATAATATGTAAAAAAATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
*
71439 CTATAAATGAC--AACAGGTAAAGCGCTACCAGATATATTGAAAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
71484 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
* * *
71549 CTATAAATGACAAAATAGGTAAAGTGCTACCAGATATATTGAAAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
*
71596 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
*
71661 CTATAAATGACAAAATAGGTAAAGCGCTACCGGATATATTGAAAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
* * *
71708 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGATAAAAAAATGACAAAACTGCT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
* *
71773 CTATAAATGACAAAACAGGTAAAGTGCTACCGAATATATTGAAAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
*
71820 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-GAAAAATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
* *
71884 CTATAAATGACAAAACAGGTAAAACGCTACCGGATATGTT-AATAGTG
66 CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAA-AGTG
71931 TCGATACTTTAT
1 TCGATACTTTAT
71943 TATAAGTATC
Statistics
Matches: 535, Mismatches: 31, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
110 106 0.20
111 68 0.13
112 361 0.67
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
CTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
Found at i:72120 original size:182 final size:182
Alignment explanation
Indices: 71814--72265 Score: 741
Period size: 182 Copynumber: 2.5 Consensus size: 182
71804 GAATATATTG
* *
71814 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTGAAAA-ATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
** *
71878 ACCGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATGTTAATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAACGCTACCGGATATGTTAATAGTGTCGATACTTTAT
*
71943 TATAAGTATCGACACTTTTGGAATTTAAAAGATAAGAAGTTATAACG-CTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGTC-AAT
* *
71995 AAAGTGTCGATACTTTATAAAAATATATCGATACATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
72060 ACCGGTCTCGAAATGACAAAACCGGTAAAGA-GCTACCGGATATGTTGAA-AGTGTCGATACTTT
66 ACCGGTCTCGAAATGACAAAACCGGTAAA-ACGCTACCGGATATGTT-AATAGTGTCGATACTTT
* *
72123 ATTATAAGTATCGACACTTTTGGAATTTAAAATAAAAGAAGTTATAGCGTCAAT
129 ATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGTCAAT
*
72177 AAATTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
*
72242 ATCGGTCTCGAAATGACAAAACCG
66 ACCGGTCTCGAAATGACAAAACCG
72266 ATAGTAAAAA
Statistics
Matches: 253, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
181 52 0.21
182 197 0.78
183 4 0.02
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAACGCTACCGGATATGTTAATAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGTCAAT
Found at i:72727 original size:23 final size:23
Alignment explanation
Indices: 72698--72745 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
72688 AAATAGGTCA
*
72698 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
* *
72721 ATATAAGCGTTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
72744 AT
1 AT
72746 TGTAATTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:74788 original size:18 final size:19
Alignment explanation
Indices: 74753--74789 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
74743 CACGGAATGT
74753 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
74773 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
74790 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:74961 original size:15 final size:15
Alignment explanation
Indices: 74943--74973 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
74933 AAATTCTAAA
74943 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
74958 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
74973 T
1 T
74974 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:82856 original size:7 final size:7
Alignment explanation
Indices: 82844--82869 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
82834 TGAAATATAC
82844 AAAGATA
1 AAAGATA
82851 AAAGATA
1 AAAGATA
82858 AAAGATA
1 AAAGATA
82865 AAAGA
1 AAAGA
82870 CCATTCTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAGATA
Found at i:87528 original size:30 final size:31
Alignment explanation
Indices: 87494--87551 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
87484 TTTTAATATT
87494 GTGTTCGAATTCATTTATTTATT-TTTGAAG
1 GTGTTCGAATTCATTTATTTATTATTTGAAG
* ** *
87524 GTGTTTGTGTTCGTTTATTTATTATTTG
1 GTGTTCGAATTCATTTATTTATTATTTG
87552 TAAATATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.17, C:0.05, G:0.19, T:0.59
Consensus pattern (31 bp):
GTGTTCGAATTCATTTATTTATTATTTGAAG
Found at i:88602 original size:55 final size:55
Alignment explanation
Indices: 88536--88714 Score: 205
Period size: 55 Copynumber: 3.1 Consensus size: 55
88526 AAAAATTTTG
* * *
88536 AACTTGAAATATTTTTAGACTTAACTCGATTGAAGCTCAAACTCAAGCTCGAAAA
1 AACTTGAAATATTTTTAGATTTAGCTCGATTGAAGCTCAAACTCGAGCTCGAAAA
* * *
88591 AACTTGAAATATTCTTAGATTTAGCTCGATTGAAGCTCAAGCTCGAGCTTGAAAAAA
1 AACTTGAAATATTTTTAGATTTAGCTCGATTGAAGCTCAAACTCGAGCTCG--AAAA
* * * * *
88648 CTTTAACTTGAAACATTTTAAGATTTAGCTCAATTGAAGTTCAAACTCGAGCTCAAAAA
1 ----AACTTGAAATATTTTTAGATTTAGCTCGATTGAAGCTCAAACTCGAGCTCGAAAA
88707 AACTTGAA
1 AACTTGAA
88715 TTGAAATATT
Statistics
Matches: 104, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
55 53 0.51
57 4 0.04
59 4 0.04
61 43 0.41
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (55 bp):
AACTTGAAATATTTTTAGATTTAGCTCGATTGAAGCTCAAACTCGAGCTCGAAAA
Found at i:88656 original size:61 final size:61
Alignment explanation
Indices: 88515--88741 Score: 245
Period size: 61 Copynumber: 3.8 Consensus size: 61
88505 CTGAAGATCG
* * *
88515 ACTCTAGCTCG-AAAAATTTTGAACTTGAAATATTTTTAGACTTAACTCGATTGAAGCTCAA
1 ACTCGAGCTCGAAAAAACTTT-AACTTGAAATATTTTTAGACTTAGCTCGATTGAAGCTCAA
* * *
88576 ACTCAAGCTCG--AAAA----AACTTGAAATATTCTTAGATTTAGCTCGATTGAAGCTCAA
1 ACTCGAGCTCGAAAAAACTTTAACTTGAAATATTTTTAGACTTAGCTCGATTGAAGCTCAA
* * * * * * *
88631 GCTCGAGCTTGAAAAAACTTTAACTTGAAACATTTTAAGATTTAGCTCAATTGAAGTTCAA
1 ACTCGAGCTCGAAAAAACTTTAACTTGAAATATTTTTAGACTTAGCTCGATTGAAGCTCAA
* * *
88692 ACTCGAGCTCAAAAAAACTTGAA-TTGAAATATTTTTAAACTTAGCTCGAT
1 ACTCGAGCTCGAAAAAACTTTAACTTGAAATATTTTTAGACTTAGCTCGAT
88742 ATATAAAAAA
Statistics
Matches: 139, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
55 45 0.32
57 4 0.03
60 26 0.19
61 64 0.46
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (61 bp):
ACTCGAGCTCGAAAAAACTTTAACTTGAAATATTTTTAGACTTAGCTCGATTGAAGCTCAA
Found at i:88959 original size:2 final size:2
Alignment explanation
Indices: 88952--88982 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
88942 ATTCAATGAT
88952 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 T
88983 TTGTATGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94895 original size:35 final size:35
Alignment explanation
Indices: 94832--94936 Score: 167
Period size: 35 Copynumber: 3.0 Consensus size: 35
94822 TTTCATTTAG
*
94832 GGGGAATCGATA-CCCCCAGGGAGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
*
94866 GGGGAATCGATACCCCCCAGGGGGGATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
*
94901 GGGGAATCGATACCCCCCAGGGGAGAATCTATTCCC
1 GGGGAATCGATACCCCCCAGGGG-GAATCTGTTCCC
94937 CCTGCACATA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
34 12 0.18
35 43 0.66
36 10 0.15
ACGTcount: A:0.22, C:0.30, G:0.30, T:0.17
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
Found at i:97845 original size:35 final size:35
Alignment explanation
Indices: 97799--97868 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
97789 TTTCATTTAG
*
97799 GGGGAATCGATACCCCCCA-GGAGGAATCTGTTCCC
1 GGGGAATCGATA-CCCCCAGGGAGGAATCTATTCCC
*
97834 GGGGAATCGATACCCCCAGGGGGGAATCTATTCCC
1 GGGGAATCGATACCCCCAGGGAGGAATCTATTCCC
97869 CCTGCACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (35 bp):
GGGGAATCGATACCCCCAGGGAGGAATCTATTCCC
Found at i:101071 original size:23 final size:23
Alignment explanation
Indices: 101045--101096 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
101035 CTATTGAAAT
*
101045 ACCACATACAAACGAACGAAGAA
1 ACCACATACAAACGAACGAAAAA
101068 ACCACATACAAACGAACGAAAAA
1 ACCACATACAAACGAACGAAAAA
101091 ACCACA
1 ACCACA
101097 CATCTGGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.58, C:0.29, G:0.10, T:0.04
Consensus pattern (23 bp):
ACCACATACAAACGAACGAAAAA
Found at i:102341 original size:23 final size:22
Alignment explanation
Indices: 102291--102353 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
102281 TTAACACTAA
*
102291 ACGAACGCTAAATGAACAGTTC
1 ACGAACACTAAATGAACAGTTC
**
102313 GTGAACACTAAATGAACATGTTC
1 ACGAACACTAAATGAACA-GTTC
* *
102336 ACGAACAATAAATAAACA
1 ACGAACACTAAATGAACA
102354 AACACAAACA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (22 bp):
ACGAACACTAAATGAACAGTTC
Found at i:103811 original size:43 final size:43
Alignment explanation
Indices: 103661--103835 Score: 226
Period size: 43 Copynumber: 4.1 Consensus size: 43
103651 TGGTAACAAA
*** * * * *
103661 AAACGCCGCAATAGGTAACGATATATAGAGGCGTTTATCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
* *
103704 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
* *
103747 AAACGCCGCAATAGGTGTTGAGATTTAGCGACGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
*
103790 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCC-AC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCG-TTTTTCCAAC
103833 AAA
1 AAA
103836 TACCGCAAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
43 111 0.94
44 7 0.06
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
Found at i:103842 original size:43 final size:43
Alignment explanation
Indices: 103702--103868 Score: 196
Period size: 43 Copynumber: 3.9 Consensus size: 43
103692 CGTTTATCCA
* *
103702 ACAAACACCGCAATAGGTGTTGATATTTAGCGGCG-TTTTTCC
1 ACAAACACCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCC
* * * *
103744 AACAAACGCCGCAATAGGTGTTGAGATTTAGCGACGTTTTTCCC
1 -ACAAACACCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCC
*
103788 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCC
1 ACAAACACCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCC
* * * *
103831 ACAAATACCGCAAAAGATC-TG-GTATATAGCGGCGTTTT
1 ACAAACACCGCAATAGGTCTTGAG-ATTTAGCGGCGTTTT
103869 ATAGAACAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 16 0.15
43 87 0.79
44 6 0.05
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (43 bp):
ACAAACACCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCC
Found at i:103878 original size:86 final size:88
Alignment explanation
Indices: 103682--103884 Score: 229
Period size: 86 Copynumber: 2.4 Consensus size: 88
103672 TAGGTAACGA
* * * *
103682 TATATAGAGGCG-TTTATCCAACAAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAA
1 TATATAGCGGCGTTTTATCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCAA
* * * *
103746 CAAACGCCGCAATAGGTGTTGAG
66 CAAACACCGCAAAAGATGCTGAG
* * *
103769 -ATTTAGCGACGTTTT-TCCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTTCC-
1 TATATAGCGGCGTTTTATCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCG-TTTTTCCA
*
103831 ACAAATACCGCAAAAGAT-CTG-G
65 ACAAACACCGCAAAAGATGCTGAG
**
103853 TATATAGCGGCGTTTTATAGAACAAACGCCGC
1 TATATAGCGGCGTTTTATCCAACAAACGCCGC
103885 TAATTACCTC
Statistics
Matches: 95, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
84 1 0.01
85 15 0.16
86 69 0.73
87 10 0.11
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (88 bp):
TATATAGCGGCGTTTTATCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCAA
CAAACACCGCAAAAGATGCTGAG
Found at i:104022 original size:21 final size:21
Alignment explanation
Indices: 103996--104036 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
103986 ATTTTCCAAT
* *
103996 AAACTTGACATCCATAACAAC
1 AAACTTAAAATCCATAACAAC
104017 AAACTTAAAATCCATAACAA
1 AAACTTAAAATCCATAACAA
104037 GAAAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (21 bp):
AAACTTAAAATCCATAACAAC
Found at i:104048 original size:21 final size:21
Alignment explanation
Indices: 104005--104054 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
103995 TAAACTTGAC
**
104005 ATCCATAACAACAAACTTAAA
1 ATCCATAACAACAAAAATAAA
* *
104026 ATCCATAACAAGAAAAATGAA
1 ATCCATAACAACAAAAATAAA
*
104047 ATACATAA
1 ATCCATAA
104055 TAATAAATCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.60, C:0.18, G:0.04, T:0.18
Consensus pattern (21 bp):
ATCCATAACAACAAAAATAAA
Found at i:106086 original size:41 final size:41
Alignment explanation
Indices: 105970--106242 Score: 166
Period size: 41 Copynumber: 6.7 Consensus size: 41
105960 ATTGCGGCGT
*
105970 TAAAGTACTATTCTATTGCGGCATTTGTATAAAAACGCCGC
1 TAAAGTACTATTCTATTGCGGCGTTTGTATAAAAACGCCGC
* *
106011 TAAAGTACTATTCTGTTGCAGCGTTTGTATAAAAACGCCGC
1 TAAAGTACTATTCTATTGCGGCGTTTGTATAAAAACGCCGC
* * * *
106052 TAAAGTACTATTCTTTTACGGCGCTTT-T-TGAAAAATGCCAC
1 TAAAGTACTATTCTATTGCGGCG-TTTGTAT-AAAAACGCCGC
* ** *** *
106093 TATAG-A-TGAACCCTATTGCAATGTTTGTATAAAAAAGCCGC
1 TAAAGTACT--ATTCTATTGCGGCGTTTGTATAAAAACGCCGC
* * ** * * * * *
106134 TAAAGTACTATT-TTTTCACGGAATTTTTTTAGAAACACCAC
1 TAAAGTACTATTCTATT-GCGGCGTTTGTATAAAAACGCCGC
** * *
106175 TATAA--A-TGAACCTATTGAGGCATTTGTATAAAAACGCCGC
1 TA-AAGTACT-ATTCTATTGCGGCGTTTGTATAAAAACGCCGC
* *
106215 TAAAGTACTACTCTGTTGCGGCGTTTGT
1 TAAAGTACTATTCTATTGCGGCGTTTGT
106243 TGAATAAACG
Statistics
Matches: 168, Mismatches: 49, Indels: 30
0.68 0.20 0.12
Matches are distributed among these distances:
39 4 0.02
40 28 0.17
41 127 0.76
42 8 0.05
43 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (41 bp):
TAAAGTACTATTCTATTGCGGCGTTTGTATAAAAACGCCGC
Found at i:106112 original size:82 final size:81
Alignment explanation
Indices: 106026--106304 Score: 278
Period size: 82 Copynumber: 3.4 Consensus size: 81
106016 TACTATTCTG
*
106026 TTGCAGCGTTTGTATAAAAACGCCGCTAAAGTACTATTCTTTTACGGCGCTTTTTGAAAAATGCC
1 TTGCAGCGTTTGTATAAAAACGCCGCTAAAGTACTATTCTTTTACGGCG-TTTTTGAAAAACGCC
106091 ACTATAGATGAACCCTA
65 ACTATAGATGAACCCTA
** * ** * * *
106108 TTGCAATGTTTGTATAAAAAAGCCGCTAAAGTACTATT-TTTTCACGGAATTTTTTTAGAAACAC
1 TTGCAGCGTTTGTATAAAAACGCCGCTAAAGTACTATTCTTTT-ACGG-CGTTTTTGAAAAACGC
*
106172 CACTATAAATGAA-CCTA
64 CACTATAGATGAACCCTA
* * * *
106189 TTG-AGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTGTTGAATAAACG
1 TTGCA-GCGTTTGTATAAAAACGCCGCTAAAGTACTATTCTTTTACGGCGTTT-TTGAA-AAACG
* *
106253 CCACTATCGATGAACCCAA
63 CCACTATAGATGAACCCTA
* * * *
106272 TTAC-GACATTTTGTATACAAACGCCGCGAAAGT
1 TTGCAG-C-GTTTGTATAAAAACGCCGCTAAAGT
106305 TACCATTTTG
Statistics
Matches: 158, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
80 4 0.03
81 45 0.28
82 81 0.51
83 6 0.04
84 22 0.14
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (81 bp):
TTGCAGCGTTTGTATAAAAACGCCGCTAAAGTACTATTCTTTTACGGCGTTTTTGAAAAACGCCA
CTATAGATGAACCCTA
Found at i:106872 original size:21 final size:20
Alignment explanation
Indices: 106832--106874 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
106822 TGGTTCATAT
106832 AAAAATAAATATTTAAATTAA
1 AAAAATAAATATTT-AATTAA
106853 AAAAATACAATAATTT-ATTAA
1 AAAAATA-AAT-ATTTAATTAA
106874 A
1 A
106875 TATTTAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 13 0.65
22 3 0.15
23 4 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATAAATATTTAATTAA
Found at i:108468 original size:35 final size:35
Alignment explanation
Indices: 108429--108563 Score: 191
Period size: 35 Copynumber: 3.8 Consensus size: 35
108419 TAAGAAGAAA
* *
108429 GAAAGAAATCATCGGCACTTTCGATTCAAGTGAAC
1 GAAAGAAAGCATTGGCACTTTCGATTCAAGTGAAC
* *
108464 GAAAGAAAGCATAGGCACTTTCGATTCAAGAAGAAC
1 GAAAGAAAGCATTGGCACTTTCGATTCAAG-TGAAC
*
108500 GAAAGGAAGCATTGGCACTTTCGATTCAAGTGAAC
1 GAAAGAAAGCATTGGCACTTTCGATTCAAGTGAAC
*
108535 GGAAGGAAA-CATTGGCACTTTCGATTCAA
1 -GAAAGAAAGCATTGGCACTTTCGATTCAA
108564 TTGTTCATCT
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
35 52 0.58
36 38 0.42
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (35 bp):
GAAAGAAAGCATTGGCACTTTCGATTCAAGTGAAC
Found at i:108497 original size:71 final size:71
Alignment explanation
Indices: 108420--108563 Score: 218
Period size: 71 Copynumber: 2.0 Consensus size: 71
108410 AAAGGTGAAT
*
108420 AAGAAGAAAGAAAGAAATCATCGGCACTTTCGATTCAAGTGAAC-GAAAGAAAGCATAGGCACTT
1 AAGAAGAAAGAAAGAAAGCATCGGCACTTTCGATTCAAGTGAACGGAAAGAAA-CATAGGCACTT
108484 TCGATTC
65 TCGATTC
* * * * *
108491 AAGAAGAACGAAAGGAAGCATTGGCACTTTCGATTCAAGTGAACGGAAGGAAACATTGGCACTTT
1 AAGAAGAAAGAAAGAAAGCATCGGCACTTTCGATTCAAGTGAACGGAAAGAAACATAGGCACTTT
108556 CGATTC
66 CGATTC
108562 AA
1 AA
108564 TTGTTCATCT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 59 0.89
72 7 0.11
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (71 bp):
AAGAAGAAAGAAAGAAAGCATCGGCACTTTCGATTCAAGTGAACGGAAAGAAACATAGGCACTTT
CGATTC
Found at i:110255 original size:35 final size:35
Alignment explanation
Indices: 110209--110343 Score: 198
Period size: 35 Copynumber: 3.8 Consensus size: 35
110199 TAAGAAGAAA
110209 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
* * *
110244 GAAAGGAAGCATCGGTACTTTCTATTCAAGAAGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAG-TGAAC
* *
110280 GAAAGGAATCATTGGCACTTTCGATTCAAGTGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
* *
110315 GGAAGGAAACATCGGCACTTTCGATTCAA
1 GAAAGGAAGCATCGGCACTTTCGATTCAA
110344 TTGTTCATCT
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
35 58 0.66
36 30 0.34
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (35 bp):
GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
Found at i:110278 original size:71 final size:71
Alignment explanation
Indices: 110200--110343 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
110190 GAAGGTGAAT
* *
110200 AAGAAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATCGGTACTTT
1 AAGAAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAACATCGGCACTTT
*
110265 CTATTC
66 CGATTC
* * * *
110271 AAGAAGAACGAAAGGAATCATTGGCACTTTCGATTCAAGTGAACGGAAGGAAACATCGGCACTTT
1 AAGAAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAACATCGGCACTTT
110336 CGATTC
66 CGATTC
110342 AA
1 AA
110344 TTGTTCATCT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (71 bp):
AAGAAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAACATCGGCACTTT
CGATTC
Found at i:112037 original size:35 final size:35
Alignment explanation
Indices: 111991--112125 Score: 198
Period size: 35 Copynumber: 3.8 Consensus size: 35
111981 TAAGAAGAAA
*
111991 GAAAGGAAGCATCGACACTTTCGATTCAAGTGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
* *
112026 GAAAGGAAGCATCGGTACTTTCGATTCAAGAAGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAG-TGAAC
* *
112062 GAAAGGAATCATTGGCACTTTCGATTCAAGTGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
* *
112097 GGAAGGAAACATCGGCACTTTCGATTCAA
1 GAAAGGAAGCATCGGCACTTTCGATTCAA
112126 TTGTTCATCT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
35 58 0.65
36 31 0.35
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (35 bp):
GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
Found at i:112060 original size:71 final size:71
Alignment explanation
Indices: 111982--112125 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
111972 GAAGGTGAAT
* *
111982 AAGAAGAAAGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGAAAGGAAGCATCGGTACTTT
1 AAGAAGAAAGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGAAAGGAAACATCGGCACTTT
112047 CGATTC
66 CGATTC
* * * * *
112053 AAGAAGAACGAAAGGAATCATTGGCACTTTCGATTCAAGTGAACGGAAGGAAACATCGGCACTTT
1 AAGAAGAAAGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGAAAGGAAACATCGGCACTTT
112118 CGATTC
66 CGATTC
112124 AA
1 AA
112126 TTGTTCATCT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (71 bp):
AAGAAGAAAGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGAAAGGAAACATCGGCACTTT
CGATTC
Found at i:116979 original size:21 final size:21
Alignment explanation
Indices: 116954--116993 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
116944 ATTTTTAATT
**
116954 ATTTTATTTAAAATATATATA
1 ATTTTATCAAAAATATATATA
116975 ATTTTATCAAAAATATATA
1 ATTTTATCAAAAATATATA
116994 CCCGTTTGAT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTATCAAAAATATATATA
Found at i:118820 original size:22 final size:23
Alignment explanation
Indices: 118778--118824 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
118768 TAAATATTTT
*
118778 AAATACCTATTTTTATAAAAAAA
1 AAATACCTATTTTAATAAAAAAA
*
118801 AAATACTTATTTTAATAAAAAAA
1 AAATACCTATTTTAATAAAAAAA
118824 A
1 A
118825 TTAAGTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATACCTATTTTAATAAAAAAA
Found at i:121612 original size:20 final size:20
Alignment explanation
Indices: 121565--121785 Score: 176
Period size: 20 Copynumber: 10.8 Consensus size: 20
121555 AATGACCAAC
* *
121565 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
121584 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
121604 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* **
121624 AAGATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
121645 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
***
121666 AAAATCGCAACGCGATTCCC
1 AAAATCGCAACGCGATTTAG
* *
121686 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTAG
**
121706 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
121727 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
**
121748 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
121769 AAGAATCGCAACGCGAT
1 AA-AATCGCAACGCGAT
121786 CTTCCAAGGA
Statistics
Matches: 159, Mismatches: 34, Indels: 15
0.76 0.16 0.07
Matches are distributed among these distances:
19 18 0.11
20 84 0.53
21 16 0.10
22 41 0.26
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:121673 original size:42 final size:42
Alignment explanation
Indices: 121622--121785 Score: 287
Period size: 42 Copynumber: 4.0 Consensus size: 42
121612 AACGTTGAAA
*
121622 AGAAGATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
* *
121664 AGAAAATCGCAACGCGA--TTCCCAGAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
121704 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
121746 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGAT
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGAT
121786 CTTCCAAGGA
Statistics
Matches: 115, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 38 0.33
42 77 0.67
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.16
Consensus pattern (42 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
Found at i:121707 original size:82 final size:83
Alignment explanation
Indices: 121621--121785 Score: 296
Period size: 82 Copynumber: 2.0 Consensus size: 83
121611 CAACGTTGAA
*
121621 AAGAAGATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGA-TTCC
1 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGACTTCC
*
121685 CAGAATCGCAACGCGATT
66 AAGAATCGCAACGCGATT
121703 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTC
1 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGA-CTTC
121768 CAAGAATCGCAACGCGAT
65 CAAGAATCGCAACGCGAT
121786 CTTCCAAGGA
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
82 59 0.75
84 20 0.25
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.16
Consensus pattern (83 bp):
AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGACTTCC
AAGAATCGCAACGCGATT
Found at i:121855 original size:6 final size:6
Alignment explanation
Indices: 121844--121986 Score: 251
Period size: 6 Copynumber: 24.7 Consensus size: 6
121834 AGACACGTAT
121844 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
121892 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
121940 GACCAC GACCAC GACCAC GACC-C GACC-C GACC-C GACC-C GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
121983 GACC
1 GACC
121987 CGAGACGAGA
Statistics
Matches: 137, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 25 0.18
6 112 0.82
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:122484 original size:6 final size:6
Alignment explanation
Indices: 122475--122517 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
122465 CGCCGCCGTC
122475 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
122518 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:122638 original size:20 final size:20
Alignment explanation
Indices: 122613--122758 Score: 86
Period size: 20 Copynumber: 7.2 Consensus size: 20
122603 GAATTTACTC
122613 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
122633 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
122653 A--TTCTTGGAATCGCATTGCG
1 ATTTTCTT--AATCGCGTTGCG
***
122673 ATTCTTGGAAGATC-CTGTTGCG
1 ATT-TTCTTA-ATCGC-GTTGCG
* * *
122695 ATCTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
* *
122715 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
* **
122735 GTTTTGAT-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
122754 ATTTT
1 ATTTT
122759 GTTGGTCATT
Statistics
Matches: 94, Mismatches: 22, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
18 4 0.04
19 17 0.18
20 54 0.57
21 7 0.07
22 10 0.11
23 2 0.02
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:122696 original size:22 final size:20
Alignment explanation
Indices: 122621--122682 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
122611 TCATTTTCTT
*
122621 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
122641 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
122661 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
122681 AA
1 AA
122683 GATCCTGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 37 0.95
21 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTTGG
Found at i:123502 original size:2 final size:2
Alignment explanation
Indices: 123495--123534 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
123485 TAATCAAATA
123495 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123535 TGCTCAGCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:125322 original size:15 final size:17
Alignment explanation
Indices: 125302--125335 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
125292 AGTTTGTAAA
125302 TTATTTG-ATAT-TAAT
1 TTATTTGTATATCTAAT
125317 TTATTTGTATATCTAAT
1 TTATTTGTATATCTAAT
125334 TT
1 TT
125336 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 4 0.24
17 6 0.35
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (17 bp):
TTATTTGTATATCTAAT
Found at i:139118 original size:31 final size:31
Alignment explanation
Indices: 139079--139184 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
139069 AATTCTTTAG
139079 GTACCAACTTGGGAGAAGATGCCTAGTTCATA
1 GTACCAACTTGGGAGAAGATGCCTAGTTCA-A
* **
139111 -TACCAACTTGGGAGCAA-AAG--TTCTTCAA
1 GTACCAACTTGGGAG-AAGATGCCTAGTTCAA
*
139139 GTACCAACTTGGGAGAAGATGCCTAGTTCAG
1 GTACCAACTTGGGAGAAGATGCCTAGTTCAA
* *
139170 GTGCTAACTTGGGAG
1 GTACCAACTTGGGAG
139185 CAAAAATTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
28 3 0.05
29 21 0.35
31 34 0.57
32 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (31 bp):
GTACCAACTTGGGAGAAGATGCCTAGTTCAA
Found at i:139164 original size:60 final size:60
Alignment explanation
Indices: 139068--139236 Score: 212
Period size: 60 Copynumber: 2.8 Consensus size: 60
139058 ATCTTTTCCT
* * *
139068 AAATTCTTTAGGTACCAACTTGGGAGAAGATGCCTAGTTCATATACCAACTTGGGAGCAA
1 AAATTCTTCAAGTACCAACTTGGGAGAAGATGCCTAGTTCATGTACCAACTTGGGAGCAA
* * * *
139128 AAGTTCTTCAAGTACCAACTTGGGAGAAGATGCCTAGTTCAGGTGCTAACTTGGGAGCAA
1 AAATTCTTCAAGTACCAACTTGGGAGAAGATGCCTAGTTCATGTACCAACTTGGGAGCAA
* * ** * * *
139188 AAATTCTTTAGGTATTAACTTAGGAAAAGATGTCTAGTTCATGTACCAA
1 AAATTCTTCAAGTACCAACTTGGGAGAAGATGCCTAGTTCATGTACCAA
139237 ATATATATTT
Statistics
Matches: 91, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 91 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (60 bp):
AAATTCTTCAAGTACCAACTTGGGAGAAGATGCCTAGTTCATGTACCAACTTGGGAGCAA
Found at i:153529 original size:59 final size:59
Alignment explanation
Indices: 153462--153586 Score: 182
Period size: 59 Copynumber: 2.1 Consensus size: 59
153452 TTTCTCAGTG
* *
153462 TGAATTTCTT-ATCATTTTAGCACAC-AAGGTGTCCAATACGGAAATTCATACACTTAGTA
1 TGAATTTCTTAAT-ATTTTAGCACACGAA-GTGCCCAATACGGAAATTCATACACTTAATA
* *
153521 TGAATTTCTTAATATTTTAGCACACGAAGTGCCCTATACTGAAATTCATACACTTAATA
1 TGAATTTCTTAATATTTTAGCACACGAAGTGCCCAATACGGAAATTCATACACTTAATA
153580 TGAATTT
1 TGAATTT
153587 TGTAACACCC
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
59 56 0.93
60 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (59 bp):
TGAATTTCTTAATATTTTAGCACACGAAGTGCCCAATACGGAAATTCATACACTTAATA
Found at i:156045 original size:59 final size:59
Alignment explanation
Indices: 155953--156080 Score: 202
Period size: 59 Copynumber: 2.2 Consensus size: 59
155943 AATTTCGTAT
* *
155953 CATTTTAGCACACAAAGTGCCCTATACTGAAATTCATACACTTAGTATGAAGTTCTTAA
1 CATTTTAGCACACAAAGTACCCTATACAGAAATTCATACACTTAGTATGAAGTTCTTAA
** * *
156012 CATTTTAGCACATGAAGTACCCTATACAGAAATTCATACACTTAGTATGTATTTCTTAA
1 CATTTTAGCACACAAAGTACCCTATACAGAAATTCATACACTTAGTATGAAGTTCTTAA
156071 CATTTTAGCA
1 CATTTTAGCA
156081 TACTTAGTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (59 bp):
CATTTTAGCACACAAAGTACCCTATACAGAAATTCATACACTTAGTATGAAGTTCTTAA
Found at i:156559 original size:94 final size:94
Alignment explanation
Indices: 156415--156637 Score: 265
Period size: 95 Copynumber: 2.4 Consensus size: 94
156405 TGGTTCTTCA
* * * *
156415 GTATCGATACTCTGACAATGGTATCGATACTACCCTACTATGATATCGATACCC-CTT-TCGATA
1 GTATCGATAC-CTTACCATGGTATCGATACTACCATACTATGATACCGATACCCTCTTCT-GATA
*
156478 TCGATACCAAAATTAGATTCGATA-TGGCATG
64 TCGATACCAAAATTAGATTCGATATTAGC-TG
* * *
156509 GTATCGATATCCTTACCATGGTATCGATACTACTATATTATTG-TACCGATACCCTCTTCTGGTA
1 GTATCGATA-CCTTACCATGGTATCGATACTACCATACTA-TGATACCGATACCCTCTTCTGATA
* *
156573 TCGATACCAAAATTAGGTTCGATATTATCTG
64 TCGATACCAAAATTAGATTCGATATTAGCTG
*
156604 GTATCGATGCCCTTACCATGGTATCGATACTACC
1 GTATCGAT-ACCTTACCATGGTATCGATACTACC
156638 TCGCGCTACC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
94 43 0.39
95 65 0.59
96 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (94 bp):
GTATCGATACCTTACCATGGTATCGATACTACCATACTATGATACCGATACCCTCTTCTGATATC
GATACCAAAATTAGATTCGATATTAGCTG
Done.