Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008840.1 Hibiscus syriacus cultivar Beakdansim tig00112044_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: 1122218
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1039685 original size:32 final size:32
Alignment explanation
Indices: 1039649--1039943 Score: 219
Period size: 32 Copynumber: 9.4 Consensus size: 32
1039639 CAATCCATAT
1039649 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1039681 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1039703 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1039735 TTTAAAATAAATCAATCCATAC-AACTAAA-TA
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* * ** * *
1039766 -AT-AAATCAATTCATAT-TTTA-AAATAAATCAA
1 TTTAAAAT-AAATCA-ATCCATACTAATAAAT-TA
* * * ** * * *
1039797 TCCATACTAATAAAT-TATTTAAAATCAATCAATCCATA
1 T--TTA-AAATAAATCAATCCATACT-AATAAAT---TA
1039835 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
1039868 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1039900 TTTAAAATAAATCAATCCATACTAATAGATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1039932 TTTAAAATAAAT
1 TTTAAAATAAAT
1039944 TATTTTAAAA
Statistics
Matches: 210, Mismatches: 25, Indels: 56
0.72 0.09 0.19
Matches are distributed among these distances:
22 16 0.08
23 1 0.00
24 1 0.00
26 3 0.01
28 3 0.01
29 8 0.04
30 11 0.05
31 9 0.04
32 116 0.55
33 4 0.02
34 4 0.02
35 3 0.01
36 22 0.10
37 7 0.03
38 1 0.00
39 1 0.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1039700 original size:54 final size:54
Alignment explanation
Indices: 1039616--1039755 Score: 262
Period size: 54 Copynumber: 2.6 Consensus size: 54
1039606 ACAACTACAA
1039616 TAATAAATTATTTAAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTT-AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1039671 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1039725 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
1039756 CAACTAAATA
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
54 71 0.85
55 13 0.15
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1039732 original size:22 final size:22
Alignment explanation
Indices: 1039683--1039731 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1039673 ATAAATTATT
**
1039683 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1039705 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
1039728 TAAA
1 TAAA
1039732 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1039765 original size:54 final size:54
Alignment explanation
Indices: 1039616--1039920 Score: 238
Period size: 54 Copynumber: 5.6 Consensus size: 54
1039606 ACAACTACAA
**
1039616 TAATAAATTATTTAAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTT-AAAATAAATCAATCCATAAATTAAAATAAATCAATCCATAC
** *
1039671 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAAATTAAAATAAATCAATCCATAC
* * *
1039725 TAATAAATTATTTAAAATAAATCAATCCATACAACT-AAAT-AATAAAT-CA-AT
1 TAATAAATTATTTAAAATAAATCAATCCATA-AATTAAAATAAATCAATCCATAC
* * ** * *
1039776 TCAT--A-T-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA--AATTAAAATAAAT-CAATCCATAC
**
1039827 -AATCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTA-TTTAAAATAAATCAAT-C---C--AT-AA--A-TTAAAATAAATCAATCCATAC
1039890 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
1039921 CTAATAGATT
Statistics
Matches: 203, Mismatches: 22, Indels: 48
0.74 0.08 0.18
Matches are distributed among these distances:
47 22 0.11
48 6 0.03
49 2 0.01
50 6 0.03
51 5 0.02
52 3 0.01
53 6 0.03
54 91 0.45
55 15 0.07
57 1 0.00
58 3 0.01
59 1 0.00
60 3 0.01
61 2 0.01
62 6 0.03
63 9 0.04
64 20 0.10
65 2 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATAAATTAAAATAAATCAATCCATAC
Found at i:1039785 original size:133 final size:133
Alignment explanation
Indices: 1039628--1039897 Score: 490
Period size: 133 Copynumber: 2.0 Consensus size: 133
1039618 ATAAATTATT
1039628 TAAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
1 TAAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
*
1039692 TCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAC
66 TCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
1039757 -AA
131 TAA
* *
1039759 CTAAATAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATCA
1 -TAAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
1039824 ATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
65 ATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1039889 CTAA
130 CTAA
1039893 TAAAT
1 TAAAT
1039898 TATTTAAAAT
Statistics
Matches: 133, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
132 4 0.03
133 127 0.95
134 2 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (133 bp):
TAAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
TCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
TAA
Found at i:1039811 original size:22 final size:23
Alignment explanation
Indices: 1039737--1039864 Score: 89
Period size: 25 Copynumber: 5.2 Consensus size: 23
1039727 ATAAATTATT
1039737 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
1039759 CTAAATAATAAATCAATTCATA-TTT
1 -T-AA-AATAAATCAATCCATACTAA
1039784 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
* * *
1039807 TAAATTATTTAAAATCAATCAATCCATATTT
1 TAAA--A--T-AAATCAATCCATAC-TA--A
1039838 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
1039861 TAAA
1 TAAA
1039865 TTATTTAAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
22 15 0.19
23 12 0.15
24 3 0.04
25 18 0.22
26 12 0.15
27 2 0.02
28 12 0.15
29 3 0.04
31 4 0.05
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:1039865 original size:22 final size:22
Alignment explanation
Indices: 1039816--1039864 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1039806 ATAAATTATT
* **
1039816 TAAAATCAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1039838 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1039861 TAAA
1 TAAA
1039865 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1039878 original size:14 final size:14
Alignment explanation
Indices: 1039859--1039958 Score: 56
Period size: 14 Copynumber: 6.5 Consensus size: 14
1039849 AATCCATACT
1039859 AATAAATTATTTAA
1 AATAAATTATTTAA
* * *
1039873 AATAAATCAATCCATACT
1 AATAAAT-TAT--TTA-A
1039891 AATAAATTATTTAA
1 AATAAATTATTTAA
* * *
1039905 AATAAATCAATCCATACT
1 AATAAAT-TAT--TTA-A
*
1039923 AATAGATTATTTAA
1 AATAAATTATTTAA
1039937 AATAAATTATTTTAA
1 AATAAATTA-TTTAA
1039952 AATAAAT
1 AATAAAT
1039959 CAATCCATAT
Statistics
Matches: 63, Mismatches: 14, Indels: 17
0.67 0.15 0.18
Matches are distributed among these distances:
14 22 0.35
15 20 0.32
17 8 0.13
18 13 0.21
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:1039951 original size:133 final size:132
Alignment explanation
Indices: 1039628--1039978 Score: 421
Period size: 133 Copynumber: 2.6 Consensus size: 132
1039618 ATAAATTATT
** *
1039628 TAAA-AATAAATC-AATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
1 TAAATAATAAATCAAAT-CATATCATAAAATAAATCAAT-CATACAAATAAATTATTTAAAATAA
*
1039691 ATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA
64 ATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1039756 CAAC
129 CAAC
* ** * *
1039760 TAAATAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATCAA
1 TAAATAATAAATCAAATCATATCATAAAATAAATCAAT-CATACAAATAAATTATTTAAAATAAA
1039825 TCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
65 TCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
1039890 TAA-
130 -AAC
* * * * *
1039893 TAAATTATTTAAAAT-AAATCA-ATCCATACTAATAGAT-TAT-TTA-AAATAAATTATTTTAAA
1 TAAA-TA-AT-AAATCAAATCATAT-CATA-AAATAAATCAATCATACAAATAAATTA-TTTAAA
*
1039953 ATAAATCAATCCATATTTTATAATAA
60 ATAAATCAATCCATATTTTAAAATAA
1039979 TTTATTTTAA
Statistics
Matches: 196, Mismatches: 14, Indels: 17
0.86 0.06 0.07
Matches are distributed among these distances:
132 13 0.07
133 155 0.79
134 8 0.04
135 10 0.05
136 10 0.05
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (132 bp):
TAAATAATAAATCAAATCATATCATAAAATAAATCAATCATACAAATAAATTATTTAAAATAAAT
CAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACA
AC
Found at i:1039952 original size:15 final size:15
Alignment explanation
Indices: 1039923--1040010 Score: 70
Period size: 15 Copynumber: 5.5 Consensus size: 15
1039913 AATCCATACT
*
1039923 AATAGATTA-TTTAA
1 AATAAATTATTTTAA
1039937 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1039952 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1039974 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
1039989 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1040004 AATAAAT
1 AATAAAT
1040011 AACCTTATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
14 8 0.13
15 35 0.58
17 1 0.02
18 2 0.03
19 3 0.05
20 1 0.02
22 10 0.17
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1039959 original size:47 final size:49
Alignment explanation
Indices: 1039891--1040010 Score: 158
Period size: 52 Copynumber: 2.4 Consensus size: 49
1039881 AATCCATACT
*
1039891 AATAAATTA-TTTAAAATAAATCAATCCATA-CTAATAGA-TTA-TTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATATATAATA-ATTTATTTTAA
1039937 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATA---TATAATAATTTATTTTAA
*
1039989 AATAAATTATTTTATAATAAAT
1 AATAAATTATTTTAAAATAAAT
1040011 AACCTTATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
46 9 0.14
47 21 0.32
50 1 0.02
51 8 0.12
52 26 0.40
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (49 bp):
AATAAATTATTTTAAAATAAATCAATCCATATATAATAATTTATTTTAA
Found at i:1040018 original size:20 final size:20
Alignment explanation
Indices: 1039995--1040064 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 20
1039985 TTAAAATAAA
1039995 TTATTTTATAATAAATAACC
1 TTATTTTATAATAAATAACC
** * ** *
1040015 TTATTAAATTAT-TTTAA-A
1 TTATTTTATAATAAATAACC
*
1040033 TTATTTTAAAATAAATAACC
1 TTATTTTATAATAAATAACC
*
1040053 ATATTTTATAAT
1 TTATTTTATAAT
1040065 TGTTCTTGAA
Statistics
Matches: 33, Mismatches: 15, Indels: 4
0.63 0.29 0.08
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 19 0.58
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTTTATAATAAATAACC
Found at i:1040033 original size:10 final size:10
Alignment explanation
Indices: 1040018--1040042 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1040008 AATAACCTTA
1040018 TTAAATTATT
1 TTAAATTATT
1040028 TTAAATTATT
1 TTAAATTATT
1040038 TTAAA
1 TTAAA
1040043 ATAAATAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAAATTATT
Found at i:1040035 original size:15 final size:14
Alignment explanation
Indices: 1039966--1040033 Score: 57
Period size: 15 Copynumber: 4.7 Consensus size: 14
1039956 AATCAATCCA
*
1039966 TATTTTATAATAATT
1 TATTTTA-AATAAAT
1039981 TATTTTAAAATAAAT
1 TATTTT-AAATAAAT
1039996 TATTTTATAATAAAT
1 TATTTTA-AATAAAT
* ** *
1040011 AACCTT-ATTAAAT
1 TATTTTAAATAAAT
1040024 TATTTTAAAT
1 TATTTTAAAT
1040034 TATTTTAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
13 9 0.22
14 3 0.07
15 28 0.68
16 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTTTAAATAAAT
Found at i:1041773 original size:2 final size:2
Alignment explanation
Indices: 1041766--1041796 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1041756 GCGGATACAA
1041766 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1041797 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1041801 original size:2 final size:2
Alignment explanation
Indices: 1041796--1041829 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1041786 ACACACACAC
1041796 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
1041830 GTATGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1046242 original size:2 final size:2
Alignment explanation
Indices: 1046237--1046262 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1046227 TTAAATTATC
1046237 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
1046263 TATTTATTTA
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:1051796 original size:33 final size:33
Alignment explanation
Indices: 1051729--1051796 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1051719 TATCAATCCA
* *
1051729 TTCTTCAATTTATTTAAAATTCTTTAATTTTTC
1 TTCTTCAATTTATTTAAAATTCTTTAAGTATTC
*
1051762 TTCTTTAATTTA-TTAAATATTCTTTAAGTATTC
1 TTCTTCAATTTATTTAAA-ATTCTTTAAGTATTC
1051795 TT
1 TT
1051797 TTCCATACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.28, C:0.10, G:0.01, T:0.60
Consensus pattern (33 bp):
TTCTTCAATTTATTTAAAATTCTTTAAGTATTC
Found at i:1052468 original size:33 final size:33
Alignment explanation
Indices: 1052431--1052511 Score: 162
Period size: 33 Copynumber: 2.5 Consensus size: 33
1052421 AATGTTGAGC
1052431 ATGTTGATGTTGATATAGTTGATAAGGCTAATA
1 ATGTTGATGTTGATATAGTTGATAAGGCTAATA
1052464 ATGTTGATGTTGATATAGTTGATAAGGCTAATA
1 ATGTTGATGTTGATATAGTTGATAAGGCTAATA
1052497 ATGTTGATGTTGATA
1 ATGTTGATGTTGATA
1052512 ATGCTAATGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.32, C:0.02, G:0.25, T:0.41
Consensus pattern (33 bp):
ATGTTGATGTTGATATAGTTGATAAGGCTAATA
Found at i:1052471 original size:18 final size:18
Alignment explanation
Indices: 1052448--1052504 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
1052438 TGTTGATATA
1052448 GTTGATAAGGCTAATAAT
1 GTTGATAAGGCTAATAAT
* *
1052466 GTTGAT---GTTGAT-AT
1 GTTGATAAGGCTAATAAT
1052480 AGTTGATAAGGCTAATAAT
1 -GTTGATAAGGCTAATAAT
1052499 GTTGAT
1 GTTGAT
1052505 GTTGATAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 2 0.07
15 10 0.33
18 16 0.53
19 2 0.07
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.39
Consensus pattern (18 bp):
GTTGATAAGGCTAATAAT
Found at i:1053483 original size:20 final size:21
Alignment explanation
Indices: 1053442--1053483 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1053432 AATCAGATTG
1053442 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
1053463 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
1053484 TGTCTAACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:1053916 original size:34 final size:34
Alignment explanation
Indices: 1053829--1053932 Score: 142
Period size: 34 Copynumber: 3.1 Consensus size: 34
1053819 TTTTGTAAAG
* *
1053829 GGGAAAGGTTCTA-TCCTAGCCCATGTAAAAGCTA
1 GGGAAAGGTTCTAGT-TTAGCCCGTGTAAAAGCTA
*
1053863 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGTTTAGCCCGTGTAAAAGCTA
*
1053897 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCGTGTAAAAGCTA
1053929 GGGA
1 GGGA
1053933 GTTTGTAAGG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
32 11 0.17
33 1 0.02
34 52 0.81
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (34 bp):
GGGAAAGGTTCTAGTTTAGCCCGTGTAAAAGCTA
Found at i:1056293 original size:21 final size:21
Alignment explanation
Indices: 1056267--1056312 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1056257 GGGGTACATT
1056267 CCCCCCAGGGGGAACAGATTC
1 CCCCCCAGGGGGAACAGATTC
* * *
1056288 CCCCCCATGGGGTACCGATTC
1 CCCCCCAGGGGGAACAGATTC
1056309 CCCC
1 CCCC
1056313 TGTCTAACGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.46, G:0.24, T:0.13
Consensus pattern (21 bp):
CCCCCCAGGGGGAACAGATTC
Found at i:1056699 original size:34 final size:34
Alignment explanation
Indices: 1056660--1056747 Score: 140
Period size: 34 Copynumber: 2.6 Consensus size: 34
1056650 TTTTGTAAAG
* *
1056660 GGGAAAGGTTCTATCTTAGCCCATGTAAAATCTA
1 GGGAAAGGTTCTAGCTTAGCCCATGTAAAATATA
*
1056694 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAATATA
1 GGGAAAGGTTCTAGCTTAGCCCATGTAAAATATA
*
1056728 GGGAAAGGTTCTAGTTTAGC
1 GGGAAAGGTTCTAGCTTAGC
1056748 TCGGAAAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTTAGCCCATGTAAAATATA
Found at i:1059565 original size:20 final size:20
Alignment explanation
Indices: 1059540--1059596 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1059530 AAATGACCAA
1059540 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGAACTC
* **
1059560 CAAATTCGCAAC-CCAGTTTC
1 CAAATTCGCAACGCGA-ACTC
1059580 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
1059597 TAGTAAATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.35, C:0.33, G:0.14, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAACTC
Found at i:1059663 original size:19 final size:20
Alignment explanation
Indices: 1059629--1059670 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1059619 CCAAATTTTT
*
1059629 AACGTGAATCTGTAAATCGC
1 AACGCGAATCTGTAAATCGC
1059649 AACGCGAAT-TGTAAATCGC
1 AACGCGAATCTGTAAATCGC
1059668 AAC
1 AAC
1059671 ACATAAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AACGCGAATCTGTAAATCGC
Found at i:1059689 original size:20 final size:20
Alignment explanation
Indices: 1059664--1059869 Score: 158
Period size: 20 Copynumber: 10.3 Consensus size: 20
1059654 GAATTGTAAA
*
1059664 TCGCAACACATAAGTTAAAT
1 TCGCAACACATAAGTCAAAT
*
1059684 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
* *
1059704 TCACAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
* *
1059724 TTGCAA-ACGTGAAGTCAAAT
1 TCGCAACACAT-AAGTCAAAT
*
1059744 TCGCAACAC-TGAACTCAAAT
1 TCGCAACACAT-AAGTCAAAT
1059764 TCGCAACAC-TGAAGTCAAAT
1 TCGCAACACAT-AAGTCAAAT
* * **
1059784 TCACAACGCGAATTTGT-AAA-
1 TCGCAACAC--ATAAGTCAAAT
*
1059804 TCGCAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
1059824 TCACAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
1059844 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
1059864 TCGCAA
1 TCGCAA
1059870 AGCGTATTTA
Statistics
Matches: 153, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
18 4 0.03
19 4 0.03
20 133 0.87
21 9 0.06
22 2 0.01
23 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:1059750 original size:60 final size:59
Alignment explanation
Indices: 1059675--1059869 Score: 179
Period size: 60 Copynumber: 3.3 Consensus size: 59
1059665 CGCAACACAT
* * * *
1059675 AAGTTAAATTCGCAACGCGATAGTCAAATTCACAACGCGATAGTCAAATTTGCAAACGTG
1 AAGTCAAATTCGCAACACGA-AGTCAAATTCACAACACGATAGTCAAATTTGCAAACGCG
* *
1059735 AAGTCAAATTCGCAACACTGAACTCAAATTCGCAACACTGA-AGTCAAA-TT-CACAACGCG
1 AAGTCAAATTCGCAACAC-GAAGTCAAATTCACAACAC-GATAGTCAAATTTGCA-AACGCG
* *
1059794 AATTTGT-AAA-TCGCAACACAAAAGTCAAATTCACAACAC-ATAAGTCAAATTCGC-AACGCG
1 AA---GTCAAATTCGCAACAC-GAAGTCAAATTCACAACACGAT-AGTCAAATTTGCAAACGCG
1059854 ATAGTCAAATTCGCAA
1 A-AGTCAAATTCGCAA
1059870 AGCGTATTTA
Statistics
Matches: 111, Mismatches: 11, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
58 5 0.05
59 12 0.11
60 82 0.74
61 9 0.08
62 3 0.03
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (59 bp):
AAGTCAAATTCGCAACACGAAGTCAAATTCACAACACGATAGTCAAATTTGCAAACGCG
Found at i:1059897 original size:19 final size:20
Alignment explanation
Indices: 1059863--1059903 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1059853 GATAGTCAAA
*
1059863 TTCGCAAAGCGTA-TTTATT
1 TTCGCAAAGCGAATTTTATT
*
1059882 TTCGCAAAGTGAATTTTATT
1 TTCGCAAAGCGAATTTTATT
1059902 TT
1 TT
1059904 ATTTTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (20 bp):
TTCGCAAAGCGAATTTTATT
Found at i:1060047 original size:22 final size:22
Alignment explanation
Indices: 1060022--1060072 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1060012 CTACGGCAAC
1060022 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
1060044 ATCCATCTCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
1060066 ATCCGTC
1 ATCCGTC
1060073 TATCTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1060439 original size:19 final size:20
Alignment explanation
Indices: 1060417--1060454 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1060407 ATTCGCAACG
1060417 CGATTTT-AGTTTCGCGTTA
1 CGATTTTCAGTTTCGCGTTA
*
1060436 CGATTTTCATTTTCGCGTT
1 CGATTTTCAGTTTCGCGTT
1060455 GTGAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.50
Consensus pattern (20 bp):
CGATTTTCAGTTTCGCGTTA
Found at i:1062005 original size:167 final size:168
Alignment explanation
Indices: 1061729--1062064 Score: 665
Period size: 167 Copynumber: 2.0 Consensus size: 168
1061719 ATGTAAGTTA
1061729 ACACACAAATACTACCATATAGTTAAACAAGTTATTTCTAGTATACGTTTAACTTTGTTTGAGCA
1 ACACACAAATACTACCATATAGTTAAACAAGTTATTTCTAGTATACGTTTAACTTTGTTTGAGCA
1061794 TTTATATTGTTAGGAGGCCAACTATCCATTACAGAGGCTGACACCCACAGAGGCTGAGCTTGCCA
66 TTTATATTGTTAGGAGGCCAACTATCCATTACAGAGGCTGACACCCACAGAGGCTGAGCTTGCCA
1061859 CTGATTGGTGGCAAGCTAGTAAGCGG-TTTTTTATGGG
131 CTGATTGGTGGCAAGCTAGTAAGCGGTTTTTTTATGGG
1061896 ACACACAAATACTACCATATAGTTAAACAAGTTATTTCTAGTATACGTTTAACTTTGTTTGAGCA
1 ACACACAAATACTACCATATAGTTAAACAAGTTATTTCTAGTATACGTTTAACTTTGTTTGAGCA
1061961 TTTATATTGTTAGGAGGCCAACTATCCATTACAGAGGCTGACACCCACAGAGGCTGAGCTTGCCA
66 TTTATATTGTTAGGAGGCCAACTATCCATTACAGAGGCTGACACCCACAGAGGCTGAGCTTGCCA
1062026 CTGATTGGTGGCAAGCTAGTAAGCGGTTTTTTTATGGG
131 CTGATTGGTGGCAAGCTAGTAAGCGGTTTTTTTATGGG
1062064 A
1 A
1062065 TGGATGATGA
Statistics
Matches: 168, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
167 156 0.93
168 12 0.07
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (168 bp):
ACACACAAATACTACCATATAGTTAAACAAGTTATTTCTAGTATACGTTTAACTTTGTTTGAGCA
TTTATATTGTTAGGAGGCCAACTATCCATTACAGAGGCTGACACCCACAGAGGCTGAGCTTGCCA
CTGATTGGTGGCAAGCTAGTAAGCGGTTTTTTTATGGG
Found at i:1062316 original size:21 final size:20
Alignment explanation
Indices: 1062292--1062473 Score: 69
Period size: 21 Copynumber: 8.7 Consensus size: 20
1062282 GTTAGGGGAG
1062292 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGT-GGTGCT
* * *
1062313 TTACGTTATGAGGTCGATACT
1 TTACGTGATGAGGT-GGTGCT
* ** *
1062334 TTACGTGAAGACAATGGTGCA
1 TTACGTGATGA-GGTGGTGCT
***
1062355 TGGTGTGATGAGGTACGGT-CT
1 TTACGTGATGAGGT--GGTGCT
* *
1062376 TTACGTGGTGAGGTGGATGTT
1 TTACGTGATGAGGTGG-TGCT
* ** *
1062397 TTACGCGATGACAATGGTGCG
1 TTACGTGATGA-GGTGGTGCT
* ** *
1062418 CTACGTGATGAGGTATCTACT
1 TTACGTGATGAGGT-GGTGCT
** *
1062439 TTACGTGATGAGGTATCTACT
1 TTACGTGATGAGGT-GGTGCT
1062460 TTACGTGATGAGGT
1 TTACGTGATGAGGT
1062474 AGCCGCTCTA
Statistics
Matches: 117, Mismatches: 37, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 105 0.90
22 7 0.06
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.33
Consensus pattern (20 bp):
TTACGTGATGAGGTGGTGCT
Found at i:1062426 original size:63 final size:65
Alignment explanation
Indices: 1062293--1062452 Score: 172
Period size: 63 Copynumber: 2.5 Consensus size: 65
1062283 TTAGGGGAGT
* *
1062293 TACGTGATGAGGT-CGGTGCTTTACGTTATGAGGTCGATACTTTACGTGAAGACAATGGTGCATG
1 TACGTGATGAGGTACGGTGCTTTACGTGATGAGGTCGATACTTTACGCGAAGACAATGGTGCA-G
*
1062357 G
65 C
* * ** *
1062358 T--GTGATGAGGTACGGT-CTTTACGTGGTGAGGTGGATGTTTTACGCGATGACAATGGTGC-GC
1 TACGTGATGAGGTACGGTGCTTTACGTGATGAGGTCGATACTTTACGCGAAGACAATGGTGCAGC
*
1062419 TACGTGATGAGGTATC--TACTTTACGTGATGAGGT
1 TACGTGATGAGGTA-CGGTGCTTTACGTGATGAGGT
1062453 ATCTACTTTA
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
61 2 0.02
62 1 0.01
63 72 0.89
64 5 0.06
65 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.34, T:0.32
Consensus pattern (65 bp):
TACGTGATGAGGTACGGTGCTTTACGTGATGAGGTCGATACTTTACGCGAAGACAATGGTGCAGC
Found at i:1062474 original size:21 final size:21
Alignment explanation
Indices: 1062419--1062474 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1062409 AATGGTGCGC
1062419 TACGTGATGAGGTATCTACTT
1 TACGTGATGAGGTATCTACTT
1062440 TACGTGATGAGGTATCTACTT
1 TACGTGATGAGGTATCTACTT
1062461 TACGTGATGAGGTA
1 TACGTGATGAGGTA
1062475 GCCGCTCTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (21 bp):
TACGTGATGAGGTATCTACTT
Found at i:1062485 original size:21 final size:21
Alignment explanation
Indices: 1062418--1062488 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
1062408 CAATGGTGCG
1062418 CTACGTGATGAGGTATCTACT
1 CTACGTGATGAGGTATCTACT
*
1062439 TTACGTGATGAGGTATCTACT
1 CTACGTGATGAGGTATCTACT
* * **
1062460 TTACGTGATGAGGTAGCCGCT
1 CTACGTGATGAGGTATCTACT
1062481 CTACGTGA
1 CTACGTGA
1062489 GATTGTTTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (21 bp):
CTACGTGATGAGGTATCTACT
Found at i:1062820 original size:42 final size:42
Alignment explanation
Indices: 1062768--1062887 Score: 118
Period size: 42 Copynumber: 2.8 Consensus size: 42
1062758 GATTCACATG
* * * *
1062768 TCATCATTCAAGAGGCGCCTCCTATCATTCAAGAGGCTC-CTC
1 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGC-CACTC
* * *
1062810 TCATCGTTCAATAGGCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCACTC
* *
1062852 TCATCGTTCAATG-GGTCCCTCCCCACCGTTCAAGAG
1 TCATCGTTCAA-GAGGCCCCT-CCCACCATTCAAGAG
1062888 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
41 1 0.02
42 50 0.76
43 15 0.23
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCACTC
Found at i:1062859 original size:21 final size:20
Alignment explanation
Indices: 1062768--1062862 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 20
1062758 GATTCACATG
*
1062768 TCATCATTCAAGAGGCGCCTC
1 TCATCGTTCAAGAGGC-CCTC
*
1062789 -CTATCATTCAAGAGGCTCCTC
1 TC-ATCGTTCAAGAGGC-CCTC
*
1062810 TCATCGTTCAATAGGCCCCTC
1 TCATCGTTCAAGAGG-CCCTC
* * *
1062831 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
1062852 TCATCGTTCAA
1 TCATCGTTCAA
1062863 TGGGTCCCTC
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
20 3 0.05
21 56 0.92
22 2 0.03
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:1064381 original size:66 final size:65
Alignment explanation
Indices: 1064220--1064395 Score: 248
Period size: 66 Copynumber: 2.6 Consensus size: 65
1064210 GGAGTACATT
*
1064220 TTTTTTTGCTTGTTTAATTGAATTTTACCTTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
1 TTTTTTTGCTTGTTTAATTG-A-TTT---GTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
*
1064285 AATTA
61 AATGA
*
1064290 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGAT-ATGTAAATAAGAAT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGA-GGAAATAAGAAT
1064353 GA
64 GA
1064355 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1064396 ATTTAAAATT
Statistics
Matches: 100, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
64 20 0.20
65 17 0.17
66 40 0.40
67 3 0.03
68 1 0.01
69 19 0.19
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.52
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATGA
Found at i:1064455 original size:20 final size:20
Alignment explanation
Indices: 1064429--1064477 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1064419 GTTGAAGGTA
* *
1064429 CAAATTCGCAATGCTAAAGGT
1 CAAATTCGCAACGCGAAA-GT
1064450 -AAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
1064469 CAAATTCGC
1 CAAATTCGC
1064478 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1067032 original size:24 final size:24
Alignment explanation
Indices: 1067005--1067081 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
1066995 CTGAAATATC
* *
1067005 ATCAAAATCCGAGTATTGATCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
1067029 ATCAAAGTCC-AGGTATTGACCAAG
1 ATCAAAGTCCGA-GTATTGACCAAG
* *
1067053 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
1067077 ATCAA
1 ATCAA
1067082 TTTCGAATAC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23
Consensus pattern (24 bp):
ATCAAAGTCCGAGTATTGACCAAG
Found at i:1067762 original size:14 final size:15
Alignment explanation
Indices: 1067726--1067763 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1067716 GAAATCATTG
1067726 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1067741 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1067756 AAAAATTA
1 AAAAATTA
1067764 GAGATAGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1067949 original size:20 final size:19
Alignment explanation
Indices: 1067926--1067973 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1067916 ACCTGTTGTG
*
1067926 AATTCGAAAATCGAGTTGCA
1 AATTTGAAAATC-AGTTGCA
* *
1067946 AATTTGAAATTCAGTTGCG
1 AATTTGAAAATCAGTTGCA
1067965 AATTTGAAA
1 AATTTGAAA
1067974 TTCATGTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (19 bp):
AATTTGAAAATCAGTTGCA
Found at i:1067961 original size:19 final size:18
Alignment explanation
Indices: 1067939--1067994 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 18
1067929 TCGAAAATCG
1067939 AGTTGCAAATTTGAAATTC
1 AGTTGC-AATTTGAAATTC
1067958 AGTTGCGAATTTGAAATTC
1 AGTTGC-AATTTGAAATTC
1067977 ATGTGTG-AATTTGAAATT
1 A-GT-TGCAATTTGAAATT
1067995 AAGTGTTGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 30 0.88
20 2 0.06
21 2 0.06
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (18 bp):
AGTTGCAATTTGAAATTC
Found at i:1068061 original size:20 final size:20
Alignment explanation
Indices: 1067997--1068065 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
1067987 TTGAAATTAA
1067997 GTGTTGCGAATTTGACTATC-
1 GTGTTGCGAATTTGACT-TCT
* *
1068017 GCGTTGCGAATTTAACTTCT
1 GTGTTGCGAATTTGACTTCT
1068037 GTGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGACTTCT
*
1068057 ATGTTGCGA
1 GTGTTGCGA
1068066 TTTACAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 2 0.05
20 41 0.95
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.41
Consensus pattern (20 bp):
GTGTTGCGAATTTGACTTCT
Found at i:1068082 original size:20 final size:20
Alignment explanation
Indices: 1068059--1068105 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1068049 TGACTTCTAT
1068059 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
1068079 GTTGCGATTTACAGATTCGT
1 GTTGCGATTTACAAATTCGC
1068099 GTTGCGA
1 GTTGCGA
1068106 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:1068390 original size:22 final size:22
Alignment explanation
Indices: 1068362--1068426 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
1068352 CTAGACCACT
1068362 AAGATCTAGGAGTCCAATATGA
1 AAGATCTAGGAGTCCAATATGA
*
1068384 AAGATCTA-GA--CC-A-CT-A
1 AAGATCTAGGAGTCCAATATGA
1068400 AA-ATCTAGGAGTCCAATATGA
1 AAGATCTAGGAGTCCAATATGA
1068421 AAGATC
1 AAGATC
1068427 AAAACATGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 3 0.09
19 3 0.09
20 1 0.03
21 5 0.15
22 11 0.32
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (22 bp):
AAGATCTAGGAGTCCAATATGA
Found at i:1068406 original size:37 final size:37
Alignment explanation
Indices: 1068352--1068426 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1068342 AGGACTTACC
*
1068352 CTAGACCACTAAGATCTAGGAGTCCAATATGAAAGAT
1 CTAGACCACTAAAATCTAGGAGTCCAATATGAAAGAT
1068389 CTAGACCACTAAAATCTAGGAGTCCAATATGAAAGAT
1 CTAGACCACTAAAATCTAGGAGTCCAATATGAAAGAT
1068426 C
1 C
1068427 AAAACATGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (37 bp):
CTAGACCACTAAAATCTAGGAGTCCAATATGAAAGAT
Found at i:1068608 original size:22 final size:23
Alignment explanation
Indices: 1068573--1068619 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1068563 GATACCAGAC
1068573 AATCAGAAGTTTCAGATCAGTAA
1 AATCAGAAGTTTCAGATCAGTAA
* *
1068596 AATCATAA-TTTCATATCAGTAA
1 AATCAGAAGTTTCAGATCAGTAA
1068618 AA
1 AA
1068620 GCAAAATTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (23 bp):
AATCAGAAGTTTCAGATCAGTAA
Found at i:1068627 original size:22 final size:22
Alignment explanation
Indices: 1068582--1068627 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1068572 CAATCAGAAG
* *
1068582 TTTCAGATCAGTAAAATCATAA
1 TTTCAGATCAGTAAAAGCAAAA
*
1068604 TTTCATATCAGTAAAAGCAAAA
1 TTTCAGATCAGTAAAAGCAAAA
1068626 TT
1 TT
1068628 CGAGAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.33
Consensus pattern (22 bp):
TTTCAGATCAGTAAAAGCAAAA
Found at i:1070947 original size:19 final size:18
Alignment explanation
Indices: 1070923--1070992 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 18
1070913 ATACTAATTG
1070923 TTTTGTAATTTTTCT-TATT
1 TTTTGT-ATTTTT-TATATT
*
1070942 TTTTGTATTTTTTGTATT
1 TTTTGTATTTTTTATATT
*
1070960 TTTTCTGATTTTTTATATT
1 TTTTGT-ATTTTTTATATT
*
1070979 TTTTATGATTTTTT
1 TTTTGT-ATTTTTT
1070993 TTAAATTCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
17 1 0.02
18 15 0.33
19 30 0.65
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (18 bp):
TTTTGTATTTTTTATATT
Found at i:1070952 original size:8 final size:9
Alignment explanation
Indices: 1070923--1070992 Score: 70
Period size: 9 Copynumber: 7.4 Consensus size: 9
1070913 ATACTAATTG
1070923 TTTTGTAATT
1 TTTTGT-ATT
1070933 TTTCT-TATT
1 TTT-TGTATT
1070942 TTTTGTATT
1 TTTTGTATT
1070951 TTTTGTATT
1 TTTTGTATT
*
1070960 TTTTCTGATT
1 TTTTGT-ATT
*
1070970 TTTTATATT
1 TTTTGTATT
*
1070979 TTTTATGATT
1 TTTTGT-ATT
1070989 TTTT
1 TTTT
1070993 TTAAATTCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
8 1 0.02
9 33 0.61
10 19 0.35
11 1 0.02
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (9 bp):
TTTTGTATT
Found at i:1070962 original size:28 final size:28
Alignment explanation
Indices: 1070923--1070992 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
1070913 ATACTAATTG
* * *
1070923 TTTTGTAATTTTTCTTATTTTTTGTATT
1 TTTTGTATTTTTTCTGATTTTTTATATT
1070951 TTTTGTATTTTTTCTGATTTTTTATATT
1 TTTTGTATTTTTTCTGATTTTTTATATT
*
1070979 TTTTATGATTTTTT
1 TTTTGT-ATTTTTT
1070993 TTAAATTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 30 0.81
29 7 0.19
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (28 bp):
TTTTGTATTTTTTCTGATTTTTTATATT
Found at i:1071513 original size:27 final size:28
Alignment explanation
Indices: 1071462--1071528 Score: 127
Period size: 27 Copynumber: 2.4 Consensus size: 28
1071452 AGACTGCCAG
1071462 ATTGTGGGCAGTGGACGTGGAGTAGTCC
1 ATTGTGGGCAGTGGACGTGGAGTAGTCC
1071490 ATTGTGGGCAGT-GACGTGGAGTAGTCC
1 ATTGTGGGCAGTGGACGTGGAGTAGTCC
1071517 ATTGTGGGCAGT
1 ATTGTGGGCAGT
1071529 TAGATTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
27 27 0.69
28 12 0.31
ACGTcount: A:0.18, C:0.13, G:0.42, T:0.27
Consensus pattern (28 bp):
ATTGTGGGCAGTGGACGTGGAGTAGTCC
Found at i:1076399 original size:51 final size:52
Alignment explanation
Indices: 1076319--1076454 Score: 148
Period size: 54 Copynumber: 2.6 Consensus size: 52
1076309 AAAATTGTAG
* * * * * * *
1076319 CACTTAACACATACTTGCACCGTTATAAGTGAATAAAAT-AAACAAGTATAT
1 CACTTAACACATACTTACACTGATGTAAGTAAATAAAATAAAAAAAGTATAA
* * *
1076370 CACTTAACACATACTTTCACTGGTGTAAGTAAATAAAATAAAAAAAAAGTGTAA
1 CACTTAACACATACTTACACTGATGTAAGTAAATAAAAT--AAAAAAAGTATAA
*
1076424 CACTTAACGCATACTTACACTGATGTAAGTA
1 CACTTAACACATACTTACACTGATGTAAGTA
1076455 TGTGCATATA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
51 34 0.48
54 37 0.52
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (52 bp):
CACTTAACACATACTTACACTGATGTAAGTAAATAAAATAAAAAAAGTATAA
Found at i:1076445 original size:54 final size:53
Alignment explanation
Indices: 1076305--1076454 Score: 160
Period size: 51 Copynumber: 2.8 Consensus size: 53
1076295 AATTCATACG
* * * * * * *
1076305 AAAAAAAATTGTAGCACTTAACACATACTTGCACCGTTATAAGTGAATAAAAT
1 AAAAAAAAGTGTAACACTTAACACATACTTACACTGATGTAAGTAAATAAAAT
* * * * *
1076358 --AAACAAGTATATCACTTAACACATACTTTCACTGGTGTAAGTAAATAAAAT
1 AAAAAAAAGTGTAACACTTAACACATACTTACACTGATGTAAGTAAATAAAAT
*
1076409 AAAAAAAAAGTGTAACACTTAACGCATACTTACACTGATGTAAGTA
1 -AAAAAAAAGTGTAACACTTAACACATACTTACACTGATGTAAGTA
1076455 TGTGCATATA
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
51 42 0.53
54 37 0.47
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (53 bp):
AAAAAAAAGTGTAACACTTAACACATACTTACACTGATGTAAGTAAATAAAAT
Found at i:1077528 original size:19 final size:19
Alignment explanation
Indices: 1077504--1077542 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1077494 GGAATATTTA
1077504 TACCGACTCTAATTAATGG
1 TACCGACTCTAATTAATGG
1077523 TACCGACTCTAATTAATGG
1 TACCGACTCTAATTAATGG
1077542 T
1 T
1077543 GTCAGACGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (19 bp):
TACCGACTCTAATTAATGG
Found at i:1077678 original size:22 final size:20
Alignment explanation
Indices: 1077618--1077680 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 20
1077608 ATATTAAATT
*
1077618 TATCAAAGATTTTTTATACT
1 TATCAAAGATTTTTTATACA
1077638 TATCAAAGATTTTTTATACA
1 TATCAAAGATTTTTTATACA
*
1077658 TATCAAAAATATTATTTATACA
1 TATCAAAGAT-TT-TTTATACA
1077680 T
1 T
1077681 TATAATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 28 0.72
21 2 0.05
22 9 0.23
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (20 bp):
TATCAAAGATTTTTTATACA
Found at i:1083546 original size:19 final size:19
Alignment explanation
Indices: 1083522--1083573 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1083512 CTCAAAAAAT
*
1083522 ATATTATTTT-ATTTATTTA
1 ATATTATTTTAATATA-TTA
*
1083541 ATATTAATTTAATATATTA
1 ATATTATTTTAATATATTA
*
1083560 GTATTATTTTAATA
1 ATATTATTTTAATA
1083574 AAATATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATTATTTTAATATATTA
Found at i:1083611 original size:38 final size:35
Alignment explanation
Indices: 1083540--1083621 Score: 83
Period size: 38 Copynumber: 2.3 Consensus size: 35
1083530 TTATTTATTT
* * **
1083540 AATATTAATTTAATATATTAGTATTATTTTAATAA
1 AATATTAATTTAAAATATTAATATTATCATAATAA
*
1083575 AATATTAATCATTAAAATATTTAATATTATCATAATAT
1 AATATTAAT--TTAAAATA-TTAATATTATCATAATAA
*
1083613 AATTTTAAT
1 AATATTAAT
1083622 AATATTATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 9 0.24
37 7 0.18
38 22 0.58
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (35 bp):
AATATTAATTTAAAATATTAATATTATCATAATAA
Found at i:1084267 original size:14 final size:14
Alignment explanation
Indices: 1084248--1084275 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1084238 TCGATTATAT
1084248 GTTCATTTATGTTC
1 GTTCATTTATGTTC
1084262 GTTCATTTATGTTC
1 GTTCATTTATGTTC
1084276 ATTTATATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:1084565 original size:13 final size:12
Alignment explanation
Indices: 1084551--1084620 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 12
1084541 TGTGTTTGTG
1084551 TTGTTCGTTTA-
1 TTGTTCGTTTAT
1084562 -TGTTCGTTTAT
1 TTGTTCGTTTAT
1084573 TGTGTTCGTTTA-
1 T-TGTTCGTTTAT
**
1084585 -TGTTAATTTAT
1 TTGTTCGTTTAT
1084596 TATGTTCGTTTAT
1 T-TGTTCGTTTAT
1084609 GTTCGTTCGTTT
1 -TT-GTTCGTTT
1084621 GTGTTCGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
10 18 0.38
13 20 0.43
14 9 0.19
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (12 bp):
TTGTTCGTTTAT
Found at i:1084567 original size:10 final size:10
Alignment explanation
Indices: 1084552--1084615 Score: 56
Period size: 10 Copynumber: 5.8 Consensus size: 10
1084542 GTGTTTGTGT
1084552 TGTTCGTTTA
1 TGTTCGTTTA
1084562 TGTTCGTTTA
1 TGTTCGTTTA
1084572 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
**
1084585 TGTTAATTTATTA
1 TGTT--CGT-TTA
1084598 TGTTCGTTTA
1 TGTTCGTTTA
1084608 TGTTCGTT
1 TGTTCGTT
1084616 CGTTTGTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 25 0.57
11 1 0.02
12 1 0.02
13 17 0.39
ACGTcount: A:0.12, C:0.08, G:0.19, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1084578 original size:23 final size:23
Alignment explanation
Indices: 1084552--1084642 Score: 121
Period size: 23 Copynumber: 3.9 Consensus size: 23
1084542 GTGTTTGTGT
1084552 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCGTTTATTG
** *
1084575 TGTTCGTTTATGTTAATTTATTA
1 TGTTCGTTTATGTTCGTTTATTG
1084598 TGTTCGTTTATGTTCGTTCGT-TTG
1 TGTTCGTTTATGTTCGTT--TATTG
*
1084622 TGTTCGTTTACGTTCGTTTAT
1 TGTTCGTTTATGTTCGTTTAT
1084643 CATTTAAATG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
22 1 0.02
23 37 0.64
24 19 0.33
25 1 0.02
ACGTcount: A:0.11, C:0.10, G:0.20, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTATGTTCGTTTATTG
Found at i:1084618 original size:14 final size:14
Alignment explanation
Indices: 1084599--1084629 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1084589 AATTTATTAT
1084599 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
1084613 GTTCGTTTGTGTTC
1 GTTCGTTTATGTTC
1084627 GTT
1 GTT
1084630 TACGTTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:1084741 original size:16 final size:16
Alignment explanation
Indices: 1084717--1084749 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1084707 AAAAAAAATT
1084717 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1084733 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1084749 T
1 T
1084750 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.24, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1085012 original size:29 final size:28
Alignment explanation
Indices: 1084980--1085039 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 28
1084970 TATTATGTTT
*
1084980 AATAT-ATAATTATTTTATAAGATTTTTTA
1 AATATAATAATTATTTTA-AAG-TATTTTA
*
1085009 AATATAATTATTATTTTAAAGTATTTTA
1 AATATAATAATTATTTTAAAGTATTTTA
1085037 AAT
1 AAT
1085040 TTTACCAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 8 0.29
30 11 0.39
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
AATATAATAATTATTTTAAAGTATTTTA
Found at i:1095007 original size:32 final size:33
Alignment explanation
Indices: 1094966--1095043 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
1094956 TTTAAATAGT
* *
1094966 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
1094998 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
1095031 TATTATTTATTTA
1 TATTATTT-TTTA
1095044 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:1095204 original size:17 final size:17
Alignment explanation
Indices: 1095182--1095235 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1095172 AATGTTAATA
1095182 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1095199 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1095216 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1095233 TTT
1 TTT
1095236 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1096796 original size:21 final size:21
Alignment explanation
Indices: 1096766--1096813 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1096756 GCAGGGGTAC
* *
1096766 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1096787 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1096808 ATGCCA
1 ATGCCA
1096814 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1096843 original size:21 final size:21
Alignment explanation
Indices: 1096817--1096889 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
1096807 TATGCCATCT
*
1096817 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
1096838 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
1096859 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
1096880 CCGCAGGGTT
1 CCGCAGGGTT
1096890 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:1097471 original size:33 final size:34
Alignment explanation
Indices: 1097412--1097508 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
1097402 AAATGTTTTT
* *
1097412 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
1097446 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
1097479 AAAATATAAATTATAGTATTCAAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
1097509 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:1097515 original size:34 final size:32
Alignment explanation
Indices: 1097410--1097515 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
1097400 ATAAATGTTT
*
1097410 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
1097444 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
1097476 TTTAAAATATAAATTATAGTATTCAAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
1097511 TTAAA
1 TTAAA
1097516 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:1098137 original size:128 final size:128
Alignment explanation
Indices: 1097909--1098664 Score: 1311
Period size: 128 Copynumber: 5.9 Consensus size: 128
1097899 TTACCTGATT
1097909 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * **** *
1097974 TGACGAAATAACGGAAGGCGCGCCCCTGGGAACGCGCCTTCATGCCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATG-TGAATAGTGAAATAATAGG
1098037 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
1098102 TGACGAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
1098165 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1098230 TAACGAAATAATGGAAGGCGCGCCCCCGGGAACGCACCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1098293 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1098358 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1098421 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1098486 TGACGAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1098549 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1098614 TGACGAAATAATGGAATGCGC-ACCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
1098665 ACTCCGATTA
Statistics
Matches: 607, Mismatches: 19, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
127 30 0.05
128 577 0.95
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1102642 original size:33 final size:33
Alignment explanation
Indices: 1102600--1102674 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
1102590 ATCGCATGCT
1102600 CTCTCTTCAACTTCCTCTTTGTTGAGATGGTTA
1 CTCTCTTCAACTTCCTCTTTGTTGAGATGGTTA
1102633 CTCTCTTCAACTTCCTCTTTGTTGAGATGGTTA
1 CTCTCTTCAACTTCCTCTTTGTTGAGATGGTTA
1102666 CTCT-TTCAA
1 CTCTCTTCAA
1102675 TTCATGATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 5 0.12
33 37 0.88
ACGTcount: A:0.16, C:0.25, G:0.13, T:0.45
Consensus pattern (33 bp):
CTCTCTTCAACTTCCTCTTTGTTGAGATGGTTA
Found at i:1103428 original size:12 final size:12
Alignment explanation
Indices: 1103371--1103428 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
1103361 AGATATATTT
* *
1103371 TATTATATTTAG
1 TATTTTATTTAA
* *
1103383 TATTTTTTTTAG
1 TATTTTATTTAA
*
1103395 TAATTTATTTAA
1 TATTTTATTTAA
1103407 -A-TTT-TTTAA
1 TATTTTATTTAA
1103416 TATTTTATTTAA
1 TATTTTATTTAA
1103428 T
1 T
1103429 TAATTGTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.13
10 4 0.11
11 4 0.11
12 25 0.66
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:1103429 original size:20 final size:21
Alignment explanation
Indices: 1103387--1103427 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1103377 ATTTAGTATT
*
1103387 TTTTTTAGTAATTTATTTAAA
1 TTTTTTAATAATTTATTTAAA
*
1103408 TTTTTTAATATTTTATTTAA
1 TTTTTTAATAATTTATTTAA
1103428 TTAATTGTTT
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:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTTTAATAATTTATTTAAA
Found at i:1103563 original size:4 final size:4
Alignment explanation
Indices: 1103554--1103578 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1103544 ATTAGTAATA
1103554 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
1103579 ATGCATGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1109549 original size:41 final size:41
Alignment explanation
Indices: 1109480--1109572 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
1109470 CCACGTAGGG
* *
1109480 TATAGCGCGGGTTAGGGGTCGCACCTGACCTTTATAATTATA
1 TATAGCGC-GGTTAAGGGCCGCACCTGACCTTTATAATTATA
**
1109522 TATAGCGCGGTTAAGGGCCGCGTCTGACCTTTATAATTATA
1 TATAGCGCGGTTAAGGGCCGCACCTGACCTTTATAATTATA
1109563 TATAGCGCGG
1 TATAGCGCGG
1109573 GGCAGGTACC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 39 0.83
42 8 0.17
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TATAGCGCGGTTAAGGGCCGCACCTGACCTTTATAATTATA
Found at i:1113227 original size:35 final size:34
Alignment explanation
Indices: 1113142--1113228 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1113132 AAAATAATTT
*
1113142 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
1113176 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
1113214 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1113229 ACTGAGATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1115486 original size:32 final size:29
Alignment explanation
Indices: 1115419--1115492 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 29
1115409 ATCTGCAAAA
* *
1115419 AAAT-TAATTAAATAAATATTAAACAATT
1 AAATATAATTAAATAAATACTAAAAAATT
1115447 AAA-ATAATTAAATAAATTACTAAAAAATACT
1 AAATATAATTAAATAAA-TACTAAAAAAT--T
*
1115478 AAATATAATAAAATA
1 AAATATAATTAAATA
1115493 CACCTTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 15 0.39
29 9 0.24
31 4 0.11
32 10 0.26
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (29 bp):
AAATATAATTAAATAAATACTAAAAAATT
Done.