Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001148.1 Hibiscus syriacus cultivar Beakdansim tig00002290_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: 95946
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:3849 original size:26 final size:26
Alignment explanation
Indices: 3788--3874 Score: 90
Period size: 25 Copynumber: 3.4 Consensus size: 26
3778 CTCTTTGGGT
*
3788 TTGGGCCTCCGGGTCCTTGTAAATC-A
1 TTGGGCCTCC-GGTACTTGTAAATCAA
* * *
3814 TTGAGTCTCCGGTTCTTGTAAATCAA
1 TTGGGCCTCCGGTACTTGTAAATCAA
3840 TTGGGCCTCC--TAACTTGTAAATCAA
1 TTGGGCCTCCGGT-ACTTGTAAATCAA
*
3865 TAGGGCCTCC
1 TTGGGCCTCC
3875 AAACTTGTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
24 1 0.02
25 34 0.65
26 17 0.33
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (26 bp):
TTGGGCCTCCGGTACTTGTAAATCAA
Found at i:3856 original size:25 final size:25
Alignment explanation
Indices: 3828--3884 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
3818 GTCTCCGGTT
* *
3828 CTTGTAAATCAATTGGGCCTCCTAA
1 CTTGTAAATCAATAGGGCCTCCAAA
3853 CTTGTAAATCAATAGGGCCTCCAAA
1 CTTGTAAATCAATAGGGCCTCCAAA
3878 CTTGTAA
1 CTTGTAA
3885 TCGAGCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (25 bp):
CTTGTAAATCAATAGGGCCTCCAAA
Found at i:3960 original size:3 final size:3
Alignment explanation
Indices: 3947--3999 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
3937 TGTAATAATT
* *
3947 TAA TAA GAA TAA TAA TAG TAA TAA TAAA TAA GTAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA -TAA TAA TAA TAA TAA
3993 TAA TAA T
1 TAA TAA T
4000 GTACTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3984 original size:11 final size:11
Alignment explanation
Indices: 3954--3997 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
3944 ATTTAATAAG
3954 AATAATAATAGT
1 AATAATAATA-T
3966 AATAATAA-AT
1 AATAATAATAT
3976 AAGTAATAATAT
1 AA-TAATAATAT
3988 AATAATAATA
1 AATAATAATA
3998 ATGTACTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.10
11 15 0.50
12 12 0.40
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (11 bp):
AATAATAATAT
Found at i:3993 original size:22 final size:22
Alignment explanation
Indices: 3956--4010 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
3946 TTAATAAGAA
3956 TAATAATAGTAATAATAAATAA-G
1 TAATAATA-TAATAAT-AATAATG
3979 TAATAATATAATAATAATAATG
1 TAATAATATAATAATAATAATG
*
4001 TACTAATATA
1 TAATAATATA
4011 TTAAACTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 5 0.17
22 17 0.57
23 8 0.27
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (22 bp):
TAATAATATAATAATAATAATG
Found at i:4007 original size:25 final size:23
Alignment explanation
Indices: 3938--4008 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 23
3928 ATTTAGGCTT
*
3938 GTAATAATTTAATAAGAATAATAATA
1 GTAATAA-TAAATAAG--TAATAATA
3964 GTAATAATAAATAAGTAATAATA
1 GTAATAATAAATAAGTAATAATA
*
3987 -TAATAAT-AATAATGTACTAATA
1 GTAATAATAAATAA-GTAATAATA
4009 TATTAAACTC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.12
22 15 0.36
23 8 0.19
25 7 0.17
26 7 0.17
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (23 bp):
GTAATAATAAATAAGTAATAATA
Found at i:4008 original size:14 final size:14
Alignment explanation
Indices: 3939--3999 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
3929 TTTAGGCTTG
*
3939 TAATAATTTAATAA
1 TAATAATATAATAA
* *
3953 GAAT-A-ATAATAG
1 TAATAATATAATAA
3965 TAATAATA-AATAA
1 TAATAATATAATAA
3978 GTAATAATATAATAA
1 -TAATAATATAATAA
3993 TAATAAT
1 TAATAAT
4000 GTACTAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 8 0.21
13 6 0.16
14 19 0.50
15 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:4791 original size:29 final size:29
Alignment explanation
Indices: 4751--4816 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
4741 TATGAAGAAC
*
4751 AAAAT-TTATAAAAAATCATTAAAAATTT
1 AAAATGTTCTAAAAAATCATTAAAAATTT
*
4779 AAAATGTTCTAAAAAATCATTAAAACTTT
1 AAAATGTTCTAAAAAATCATTAAAAATTT
4808 AAAATGTTC
1 AAAATGTTC
4817 ACCATAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 5 0.14
29 30 0.86
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATGTTCTAAAAAATCATTAAAAATTT
Found at i:7865 original size:20 final size:21
Alignment explanation
Indices: 7840--7885 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
7830 CCTTACAGTG
* *
7840 TCAATAAC-TTCTCTATAGTA
1 TCAATAACATTCTCTACAATA
7860 TCAAT-ACATTCTCTACAATA
1 TCAATAACATTCTCTACAATA
7880 TCAATA
1 TCAATA
7886 CCCTTCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (21 bp):
TCAATAACATTCTCTACAATA
Found at i:11323 original size:24 final size:24
Alignment explanation
Indices: 11296--11369 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
11286 AAAACAATTA
11296 AGGGAATTATCTTTTGTGATTTTT
1 AGGGAATTATCTTTTGTGATTTTT
* *
11320 AGGGAATTATCTTTTATAATTTTT
1 AGGGAATTATCTTTTGTGATTTTT
*
11344 A-GGAATTA--TTTTGAGCATTTTT
1 AGGGAATTATCTTTTGTG-ATTTTT
11366 AGGG
1 AGGG
11370 TTTTAGGATG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.09
22 7 0.16
23 9 0.21
24 23 0.53
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (24 bp):
AGGGAATTATCTTTTGTGATTTTT
Found at i:38410 original size:39 final size:39
Alignment explanation
Indices: 38367--38485 Score: 111
Period size: 39 Copynumber: 3.1 Consensus size: 39
38357 TTTAAACAAT
* *
38367 AATTTAGAATATTAATGTGAAATAATTTAAGGAATTAAA
1 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAA
* * **
38406 AATTTAGAATGTT-ATGGTAGCAA-AATTTAATAAATTATG
1 AATTTAGAATGTTAAT-GT-GAAATAATTTAAGAAATTAAA
* *
38445 AATTTAGAATGTTAGA-GTGAAATAATTTGA-AAATTATA
1 AATTTAGAATGTTA-ATGTGAAATAATTTAAGAAATTAAA
38483 AAT
1 AAT
38486 AAAAATTAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
38 15 0.23
39 47 0.71
40 3 0.05
41 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.37
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAA
Found at i:39610 original size:12 final size:12
Alignment explanation
Indices: 39593--39618 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39583 CATATAACAA
39593 TATATAATTATT
1 TATATAATTATT
39605 TATATAATTATT
1 TATATAATTATT
39617 TA
1 TA
39619 GTTTTTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATAATTATT
Found at i:43045 original size:3 final size:3
Alignment explanation
Indices: 43026--43100 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
43016 GCAAAATATG
* * *
43026 TAA TAA TAC TAA GTAA TAA TAA TAA TAA TAA TGTA TTA TAA T-A TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
43072 TAG TTA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43101 GATAATTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
2 4 0.07
3 51 0.85
4 5 0.08
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:43080 original size:14 final size:14
Alignment explanation
Indices: 43039--43100 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
43029 TAATACTAAG
43039 TAATAATAATA--A
1 TAATAATAATATTA
*
43051 TAATAAT-GTATTA
1 TAATAATAATATTA
43064 TAAT-ATAATAGTTA
1 TAATAATAATA-TTA
*
43078 TAATAATAATATAA
1 TAATAATAATATTA
43092 TAATAATAA
1 TAATAATAA
43101 GATAATTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.05
12 9 0.21
13 7 0.17
14 18 0.43
15 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
TAATAATAATATTA
Found at i:43106 original size:11 final size:11
Alignment explanation
Indices: 43026--43099 Score: 73
Period size: 11 Copynumber: 6.7 Consensus size: 11
43016 GCAAAATATG
43026 TAATAATACTAA
1 TAATAATA-TAA
43038 GTAATAATAATAA
1 -TAATAAT-ATAA
*
43051 TAATAATGT-A
1 TAATAATATAA
*
43061 TTATAATATAA
1 TAATAATATAA
*
43072 TAGT--TATAA
1 TAATAATATAA
43081 TAATAATATAA
1 TAATAATATAA
43092 TAATAATA
1 TAATAATA
43100 AGATAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
9 8 0.16
10 8 0.16
11 17 0.33
12 7 0.14
13 10 0.20
14 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (11 bp):
TAATAATATAA
Found at i:43113 original size:14 final size:14
Alignment explanation
Indices: 43026--43106 Score: 59
Period size: 13 Copynumber: 6.3 Consensus size: 14
43016 GCAAAATATG
*
43026 TAATAATACTAAG-
1 TAATAATAATAAGA
43039 TAATAATAAT-A-A
1 TAATAATAATAAGA
* **
43051 TAATAAT-GTATTA
1 TAATAATAATAAGA
43064 TAAT-ATAAT-AG-
1 TAATAATAATAAGA
* *
43075 TTATAATAATAATA
1 TAATAATAATAAGA
43089 TAATAATAATAAGA
1 TAATAATAATAAGA
43103 TAAT
1 TAAT
43107 TTTAATATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 13
0.69 0.14 0.18
Matches are distributed among these distances:
11 4 0.08
12 15 0.29
13 16 0.31
14 16 0.31
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (14 bp):
TAATAATAATAAGA
Found at i:43462 original size:55 final size:55
Alignment explanation
Indices: 43370--44320 Score: 1233
Period size: 55 Copynumber: 17.5 Consensus size: 55
43360 CTTTTTTAGG
* *
43370 GAGTATAA-ATCTCGAACAA-CTTCAACAATCGTGTTTGCTCCCTATTCCTTTAGA
1 GAGTATAAGA-CTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * * * *
43424 AAGTATAAGACTCGAAGAACCTTCAACAATCGTTTTTGCTCACTATTCTTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * *
43479 GAGTATAAGACTCGAACAATCTTCAACAATCGTGCCCGCTCTCTATTCGTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
43534 GAGTATAAGACTCGAATAATGTTCAACAATCGTGTCCT-CTCCCTATTCCTTCAGG
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGT-CTGCTCCCTATTCCTTCAGA
* * * *
43589 GAGTATAAGACTCAAACAACCTTCAATAATCGTGTTTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
*
43644 GAGTATAAGACTCGAACAACCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* *
43699 GAGTATAAGACTCGAACAATCTTCAACAATCATGTCTGCTCACTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * *
43754 GAGTATGAGACTTGAACAATCTTCAACAAACGTGTCTGCTCTCTATTCCTTTAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * *
43809 GAG--T---ACTCGAGCAATCTTCAACAATCGTGTTTTCTCCCTATTTCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * * *
43859 GAGTATTAGACTCGAACAATTTTTAACATTTGTGTCTGCTCCCTATTTCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * * *
43914 GAGTATGAGACTCGAACAATATTAAACATTCGTGTTTGCTCCCTATTTCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* *
43969 GAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * *
44024 GAGTATATGACTCAAACAA---TCAATAATCGTGTCCGCTCCCTATTTCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
44076 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCCGCTCTCTATTCTTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* *
44131 GAGTATAAGACTTGAATAATCTTCAACAATCGTGT-TGGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT-GCTCCCTATTCCTTCAGA
* *
44186 GAGTATAAGACTTGAACAACCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
44241 GAGTATAAGACTCGAACAACCTTCAACAATCGTTTCCGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
*
44296 GAGTATAAGACCCGAACAATCTTCA
1 GAGTATAAGACTCGAACAATCTTCA
44321 TTTGCTTCAC
Statistics
Matches: 795, Mismatches: 88, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
50 41 0.05
52 49 0.06
53 1 0.00
54 16 0.02
55 686 0.86
56 2 0.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (55 bp):
GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
Found at i:44693 original size:37 final size:37
Alignment explanation
Indices: 44672--44803 Score: 185
Period size: 37 Copynumber: 3.6 Consensus size: 37
44662 ACTCTTTCGA
*
44672 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTCAGT
1 GAAGGCTTAAGATGGATTTGCTTCACTACTCTTCAGT
* * *
44709 GAAGGCTTAAGATGGATTTGTTTCACTACACTTCGGT
1 GAAGGCTTAAGATGGATTTGCTTCACTACTCTTCAGT
* *
44746 GAAGGCTTAAGATGGATTTGCTTCACTATTTTTC-GT
1 GAAGGCTTAAGATGGATTTGCTTCACTACTCTTCAGT
*
44782 GAAGGCTTAAGATTGACTTTGC
1 GAAGGCTTAAGATGGA-TTTGC
44804 CCCAATCTCC
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
36 17 0.20
37 68 0.80
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (37 bp):
GAAGGCTTAAGATGGATTTGCTTCACTACTCTTCAGT
Found at i:51853 original size:6 final size:6
Alignment explanation
Indices: 51841--51912 Score: 117
Period size: 6 Copynumber: 12.0 Consensus size: 6
51831 CAAAAATAAG
* *
51841 AATGCA GATGCA GATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
*
51889 AATGCA AATGCA AATGTA AATGCA
1 AATGCA AATGCA AATGCA AATGCA
51913 CGAGGTGTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.18
Consensus pattern (6 bp):
AATGCA
Found at i:56192 original size:3 final size:3
Alignment explanation
Indices: 56184--56250 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
56174 GCAAAATATG
* *
56184 TAA TAA TAA TAA GTAA TAA TAA TAA TAA TAA TGTA TTA TAA T-A TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
56230 TAG TTA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
56251 TTTAATATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.07
3 45 0.83
4 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:56199 original size:13 final size:13
Alignment explanation
Indices: 56178--56244 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 13
56168 GGTGCTGCAA
*
56178 AATATGTAATAAT
1 AATAAGTAATAAT
56191 AATAAGTAATAAT
1 AATAAGTAATAAT
56204 AATAA-TAATAAT
1 AATAAGTAATAAT
* *
56216 GTATTA-TAAT-AT
1 -AATAAGTAATAAT
*
56228 AAT-AGTTATAAT
1 AATAAGTAATAAT
56240 AATAA
1 AATAA
56245 TATAATTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
10 1 0.02
11 5 0.11
12 14 0.31
13 25 0.56
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (13 bp):
AATAAGTAATAAT
Found at i:56208 original size:19 final size:18
Alignment explanation
Indices: 56184--56246 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
56174 GCAAAATATG
56184 TAATAATAATAAGTAATAA
1 TAATAATAATAAGT-ATAA
*
56203 TAATAATAATAATGTATTA
1 TAATAATAATAA-GTATAA
56222 TAAT-ATAAT-AGTTATAA
1 TAATAATAATAAG-TATAA
56239 TAATAATA
1 TAATAATA
56247 TAATTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.03
17 9 0.23
18 8 0.21
19 19 0.49
20 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
TAATAATAATAAGTATAA
Found at i:56212 original size:22 final size:20
Alignment explanation
Indices: 56186--56250 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
56176 AAAATATGTA
56186 ATAATAATAAGTAATAATAAT
1 ATAATAAT-AGTAATAATAAT
*
56207 AATAATAAT-GT-ATTATAAT
1 -ATAATAATAGTAATAATAAT
*
56226 ATAATAGTTA-TAATAATAAT
1 ATAATA-ATAGTAATAATAAT
56246 ATAAT
1 ATAAT
56251 TTTAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 6 0.16
19 9 0.24
20 14 0.38
22 8 0.22
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
ATAATAATAGTAATAATAAT
Found at i:56238 original size:14 final size:14
Alignment explanation
Indices: 56184--56269 Score: 57
Period size: 14 Copynumber: 5.9 Consensus size: 14
56174 GCAAAATATG
* *
56184 TAATAATAATAA-G
1 TAATAATTATAATA
*
56197 TAATAATAATAATAA
1 TAATAATTATAAT-A
*
56212 TAATGTATTATAATA
1 TAAT-AATTATAATA
*
56227 TAATAGTTATAATAA
1 TAATAATTATAAT-A
*
56242 TAATATAATTTTAATA
1 T-A-ATAATTATAATA
*
56258 TAATATTTATAA
1 TAATAATTATAA
56270 CCCGGACAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
13 12 0.21
14 15 0.26
15 12 0.21
16 10 0.17
17 9 0.16
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TAATAATTATAATA
Found at i:56246 original size:36 final size:31
Alignment explanation
Indices: 56205--56269 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
56195 AGTAATAATA
* *
56205 ATAATAATAATGT-ATTATAATATAATAGTT
1 ATAATAATAATATAATTTTAATATAATAGTT
*
56235 ATAATAATAATATAATTTTAATATAATATTT
1 ATAATAATAATATAATTTTAATATAATAGTT
56266 ATAA
1 ATAA
56270 CCCGGACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (31 bp):
ATAATAATAATATAATTTTAATATAATAGTT
Found at i:57871 original size:20 final size:20
Alignment explanation
Indices: 57846--57884 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
57836 GTTGAAACCA
57846 ATGATGACGATGAAGACAAG
1 ATGATGACGATGAAGACAAG
*
57866 ATGATGACGATGATGACAA
1 ATGATGACGATGAAGACAA
57885 CGAGGATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.28, T:0.18
Consensus pattern (20 bp):
ATGATGACGATGAAGACAAG
Found at i:58139 original size:12 final size:12
Alignment explanation
Indices: 58088--58141 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
58078 TTGTATCAAG
*
58088 TTTTTATGTTTC
1 TTTTTATGTTTT
58100 TTTTTATGTATTT
1 TTTTTATGT-TTT
**
58113 ATTATTTATCATTT
1 -TT-TTTATGTTTT
58127 TTTTTATGTTTT
1 TTTTTATGTTTT
58139 TTT
1 TTT
58142 CGCTTATTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 20 0.59
13 4 0.12
14 5 0.15
15 5 0.15
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.76
Consensus pattern (12 bp):
TTTTTATGTTTT
Found at i:59911 original size:83 final size:82
Alignment explanation
Indices: 59806--60201 Score: 409
Period size: 83 Copynumber: 4.8 Consensus size: 82
59796 ATAATAGTAA
* ** * ** *
59806 TTCATCTTATCTGAAATGAAAGGTGTGTTTCGAGAGAAGTGTTTTCCATTATTATTTAGAGAATC
1 TTCATCTCATCTGAAATGAAAGGTGCATTTCG-GGGAAACGTTTTCCATTATTATTCAGAGAATC
59871 TCTTCCATGTCAGAGTGT
65 TCTTCCATGTCAGAGTGT
* * *
59889 TTCATCTCATCTGAAATAAAAGGTGCATTTTGGGGAAATCGTTTTCCATTATTATTCAAAGAATC
1 TTCATCTCATCTGAAATGAAAGGTGCATTTCGGGGAAA-CGTTTTCCATTATTATTCAGAGAATC
*
59954 TCTTCCATGTCAAAGTGT
65 TCTTCCATGTCAGAGTGT
* * * *** * * * *
59972 TACATCCCATCTAAAATGAAAGACACATTTCAGGGAAAACATTTTCTATTATTATTCAGAGAATT
1 TTCATCTCATCTGAAATGAAAGGTGCATTTC-GGGGAAACGTTTTCCATTATTATTCAGAGAATC
* *
60037 TATGCCATGTCAGAGTGT
65 TCTTCCATGTCAGAGTGT
* * * * *
60055 TCCATCTCATTTGAAATGAAAGGCGCATTTTGGGGAAAGCGTTTTCCAATATTATTCAGAGAATC
1 TTCATCTCATCTGAAATGAAAGGTGCATTTCGGGGAAA-CGTTTTCCATTATTATTCAGAGAATC
*
60120 TCTAT-CATGTTAGAGTG-
65 TCT-TCCATGTCAGAGTGT
* * * * *
60137 TTCTATCTCATTTGAAATGAAAAGTGAATTTCGGGGAAAACGTATTCCATTATTATTTAGAGAAT
1 TTC-ATCTCATCTGAAATGAAAGGTGCATTTCGGGG-AAACGTTTTCCATTATTATTCAGAGAAT
60202 ATATGTCATG
Statistics
Matches: 257, Mismatches: 50, Indels: 12
0.81 0.16 0.04
Matches are distributed among these distances:
82 12 0.05
83 236 0.92
84 9 0.04
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (82 bp):
TTCATCTCATCTGAAATGAAAGGTGCATTTCGGGGAAACGTTTTCCATTATTATTCAGAGAATCT
CTTCCATGTCAGAGTGT
Found at i:60047 original size:166 final size:166
Alignment explanation
Indices: 59847--60223 Score: 481
Period size: 166 Copynumber: 2.3 Consensus size: 166
59837 GAGAGAAGTG
* * * *
59847 TTTTCCATTATTATTTAGAGAATCTCTTCCATGTCAGAGTGTTTCATCTCATCTGAAATAAAAGG
1 TTTTCCATTATTATTTAGAGAATATATGCCATGTCAGAGTGTTCCATCTCATCTGAAATAAAAGG
* * *
59912 TGCATTTTGGGGAAATCGTTTTCCATTATTATTCAAAGAATCTCT-TCCATGTCAAAGTGTTAC-
66 CGCATTTTGGGGAAAGCGTTTTCCAATATTATTCAAAGAATCTCTAT-CATGTCAAAGTGTT-CT
59975 ATCCCATCTAAAATG-AAAGACACATTTCAGGGAAAACA
129 ATCCCATCTAAAATGAAAAGACA-ATTTCAGGGAAAACA
* * * * *
60013 TTTTCTATTATTATTCAGAGAATTTATGCCATGTCAGAGTGTTCCATCTCATTTGAAATGAAAGG
1 TTTTCCATTATTATTTAGAGAATATATGCCATGTCAGAGTGTTCCATCTCATCTGAAATAAAAGG
* * *
60078 CGCATTTTGGGGAAAGCGTTTTCCAATATTATTCAGAGAATCTCTATCATGTTAGAGTGTTCTAT
66 CGCATTTTGGGGAAAGCGTTTTCCAATATTATTCAAAGAATCTCTATCATGTCAAAGTGTTCTAT
* * * ** * *
60143 CTCATTTGAAATGAAAAGTGAATTTCGGGGAAAACG
131 CCCATCTAAAATGAAAAGACAATTTCAGGGAAAACA
* * *
60179 TATTCCATTATTATTTAGAGAATATATGTCATGTCAAAGTGTTCC
1 TTTTCCATTATTATTTAGAGAATATATGCCATGTCAGAGTGTTCC
60224 GTTAACATAT
Statistics
Matches: 181, Mismatches: 27, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
165 1 0.01
166 174 0.96
167 6 0.03
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (166 bp):
TTTTCCATTATTATTTAGAGAATATATGCCATGTCAGAGTGTTCCATCTCATCTGAAATAAAAGG
CGCATTTTGGGGAAAGCGTTTTCCAATATTATTCAAAGAATCTCTATCATGTCAAAGTGTTCTAT
CCCATCTAAAATGAAAAGACAATTTCAGGGAAAACA
Found at i:64535 original size:462 final size:459
Alignment explanation
Indices: 63674--64593 Score: 1705
Period size: 462 Copynumber: 2.0 Consensus size: 459
63664 TCAATGTTTG
*
63674 TAAGGAATATTAAGATCAAAATCCAATGCTTTCTTGGGTAGGTTGTCTTTGTTATCAACTCCAGC
1 TAAGGAATATTAAGATCAAAATCCAATGCTTTCTTGGGGAGGTTGTCTTTGTTATCAACTCCAGC
* * *
63739 TTCATTTTTTTGGTCTTGTACTGTTAACTTACTGGTGGTGATCAATGCAGTCGCCACATTGTTGA
66 TTCATTTTTTGGGTCTTGCACTGTTAACGTACTGGTGGTGATCAATGCAGTCGCCACATTGTTGA
*
63804 TCCTTCCATGGCCGACCCCACTTATGAAATTGTCAGCGTTGCAAGCACTCCCAACTTCTTCTTCT
131 TCCTTCCAAGGCCGACCCCACTTATGAAATTGTCAGCGTTGCAAGCACTCCCAACTTCTTCTTCT
* * *
63869 TTGAAATTTCCTCTTTGTGGGGAATTCGTTTCCAAGATTTGTGATTCTTGTTGATTCTTTTCTGC
196 TTAAAATTTCCTCTTTGTGGGGAATCCGTTTCCAAGATTTGTGATTCATGTTGATTCTTTTCTGC
63934 AACTCCACTGATATGAAGCTTCTTGGCTTCTCGACCTCTCTTTCCGGTGACTAACCAGTTGGGTA
261 AACTCCACTGATATGAAGCTTCTTGGCTTCTCGACCTCTCTTTCCGGTGACTAACCAGTTGGGTA
63999 ATCCATCTAACAAGTTGATTACGTCAGGCTTTAGTTGAGGCCTGACACTGTTCCAGTTGTTATCT
326 ATCCATCTAACAAGTTGATTACGTCAGGCTTTAGTTGAGGCCTGACACTGTTCCAGTTGTTATCT
*
64064 TTCTTCATCTTGCGGGTGATCGGGAAAGGGGGATATTCATCGTCTCCGGCAGCATCTTGGGGCTT
391 TTCTTCATCTTGCGGGTGATCGGGAAAGGGGGATATTCATCGTCTCCGGCAGCATCTTGGAGCTT
64129 TTTA
456 TTTA
*
64133 TAAGGAATATTAAGATCAAAATCCAATGCTTTCTTGGGGAGGTTGTCTTTGTTATCAACTCCTGC
1 TAAGGAATATTAAGATCAAAATCCAATGCTTTCTTGGGGAGGTTGTCTTTGTTATCAACTCCAGC
*
64198 TTCATTTTTTGGGTGTTGCACTGTTAACGTACTGGTGGTGATCAATGCAGTCGCCACATTGTTGA
66 TTCATTTTTTGGGTCTTGCACTGTTAACGTACTGGTGGTGATCAATGCAGTCGCCACATTGTTGA
64263 TCCTTCCAAGGCCGACCCCACTTATGAAATTGTCAGCGTTGCAAGCACTCCCAACTTCTTCTTCT
131 TCCTTCCAAGGCCGACCCCACTTATGAAATTGTCAGCGTTGCAAGCACTCCCAA---CTTCTTCT
*
64328 TCTTTAAAATTTCCTCTTTGTGGGGAATCCGTTTCCAAGATTTGTGATTCATGTTGGTTCTTTTC
193 TCTTTAAAATTTCCTCTTTGTGGGGAATCCGTTTCCAAGATTTGTGATTCATGTTGATTCTTTTC
64393 TGCAACTCCACTGATATGAAGCTTCTTGGCTTCTCGACCTCTCTTTCCGGTGACTAACCAGTTGG
258 TGCAACTCCACTGATATGAAGCTTCTTGGCTTCTCGACCTCTCTTTCCGGTGACTAACCAGTTGG
64458 GTAATCCATCTAACAAGTTGATTACGTCAGGCTTTAGTTGAGGCCTGACACTGTTCCAGTTGTTA
323 GTAATCCATCTAACAAGTTGATTACGTCAGGCTTTAGTTGAGGCCTGACACTGTTCCAGTTGTTA
64523 TCTTTCTTCATCTTGCGGGTGATCGGGAAAGGGGGATATTCATCGTCTCCGGCAGCATCTTGGAG
388 TCTTTCTTCATCTTGCGGGTGATCGGGAAAGGGGGATATTCATCGTCTCCGGCAGCATCTTGGAG
64588 CTTTTT
453 CTTTTT
64594 GTGGACCCGA
Statistics
Matches: 446, Mismatches: 12, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
459 177 0.40
462 269 0.60
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (459 bp):
TAAGGAATATTAAGATCAAAATCCAATGCTTTCTTGGGGAGGTTGTCTTTGTTATCAACTCCAGC
TTCATTTTTTGGGTCTTGCACTGTTAACGTACTGGTGGTGATCAATGCAGTCGCCACATTGTTGA
TCCTTCCAAGGCCGACCCCACTTATGAAATTGTCAGCGTTGCAAGCACTCCCAACTTCTTCTTCT
TTAAAATTTCCTCTTTGTGGGGAATCCGTTTCCAAGATTTGTGATTCATGTTGATTCTTTTCTGC
AACTCCACTGATATGAAGCTTCTTGGCTTCTCGACCTCTCTTTCCGGTGACTAACCAGTTGGGTA
ATCCATCTAACAAGTTGATTACGTCAGGCTTTAGTTGAGGCCTGACACTGTTCCAGTTGTTATCT
TTCTTCATCTTGCGGGTGATCGGGAAAGGGGGATATTCATCGTCTCCGGCAGCATCTTGGAGCTT
TTTA
Found at i:71909 original size:114 final size:114
Alignment explanation
Indices: 71770--72173 Score: 553
Period size: 114 Copynumber: 3.5 Consensus size: 114
71760 TAGCCCAAAC
* * * *
71770 TTAACTATTTAAGTCATTTTATTTTCAGTGAAATATCGCATAAAATCATAACTTCTTTCATAATG
1 TTAACTATTCAAGTCATTTTCTTTTCAGTGAAATATCACATAAAATCAAAACTTCTTTCATAATG
* *
71835 AATGAAAAATCTTATCAGATACAATAATAATTTCAAATGATAAAGAACT
66 AATGAAAAATCTTATCAGATACAATAATAATTTCAAATGACAGAGAACT
* * * *
71884 TTAACTATTCAAGTCATTTTCTTTTCAATGAAATATCACATAAAATTAGAACTTCTTTCATACTG
1 TTAACTATTCAAGTCATTTTCTTTTCAGTGAAATATCACATAAAATCAAAACTTCTTTCATAATG
* * * *
71949 AATGAAAAATCTTTTCCGGTACAATAATAATTTCAAATGACAGAGAATT
66 AATGAAAAATCTTATCAGATACAATAATAATTTCAAATGACAGAGAACT
* * *
71998 TTAACTATTCAAGTTC-TTTTCTTTTCAGTGAAATATCACATCAAATCAAAACTTCTTTTATAGT
1 TTAACTATTCAAG-TCATTTTCTTTTCAGTGAAATATCACATAAAATCAAAACTTCTTTCATAAT
* * *
72062 AAATGAAAAATCTTATCTA-ATATAATTATAATTTCAAATGACAGAGAATCT
65 GAATGAAAAATCTTATC-AGATACAATAATAATTTCAAATGACAGAGAA-CT
* * *
72113 TT-ATTATTCAAGTCCTTTTCTTTTCAGTGAAATATCACATCAAATCAAAACTTCTTTCATA
1 TTAACTATTCAAGTCATTTTCTTTTCAGTGAAATATCACATAAAATCAAAACTTCTTTCATA
72174 GTAATATAAT
Statistics
Matches: 258, Mismatches: 28, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
113 2 0.01
114 251 0.97
115 5 0.02
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (114 bp):
TTAACTATTCAAGTCATTTTCTTTTCAGTGAAATATCACATAAAATCAAAACTTCTTTCATAATG
AATGAAAAATCTTATCAGATACAATAATAATTTCAAATGACAGAGAACT
Found at i:72857 original size:25 final size:25
Alignment explanation
Indices: 72829--72880 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
72819 ATTTACCATA
* *
72829 TTTATATTATGTTTTATTTATGAAG
1 TTTATATGATGTTTTATTTATCAAG
*
72854 TTTATGTGATGTTTTATTTATCAAG
1 TTTATATGATGTTTTATTTATCAAG
72879 TT
1 TT
72881 CATAATGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.13, T:0.60
Consensus pattern (25 bp):
TTTATATGATGTTTTATTTATCAAG
Found at i:73300 original size:17 final size:17
Alignment explanation
Indices: 73255--73300 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
73245 ATTATTTTTC
*
73255 TTAATAATTTTATAAAAA
1 TTAA-AATTTTCTAAAAA
*
73273 TTAAAATTTTCTAAAAT
1 TTAAAATTTTCTAAAAA
73290 TTAAAATTTTC
1 TTAAAATTTTC
73301 ATTTTCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAAATTTTCTAAAAA
Found at i:76329 original size:17 final size:18
Alignment explanation
Indices: 76297--76331 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
76287 ATACCTTACT
76297 ATAAAGATAATAGTATGG
1 ATAAAGATAATAGTATGG
*
76315 ATAAA-ATAATGGTATGG
1 ATAAAGATAATAGTATGG
76332 TATATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (18 bp):
ATAAAGATAATAGTATGG
Found at i:77589 original size:2 final size:2
Alignment explanation
Indices: 77582--77614 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
77572 TTTTAATTTC
77582 AT AT AT AT AT AT -T 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
77615 CAATCATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:78241 original size:7 final size:7
Alignment explanation
Indices: 78226--78277 Score: 95
Period size: 7 Copynumber: 7.4 Consensus size: 7
78216 ACAAATTCTA
*
78226 AAATGAT
1 AAATTAT
78233 AAATTAT
1 AAATTAT
78240 AAATTAT
1 AAATTAT
78247 AAATTAT
1 AAATTAT
78254 AAATTAT
1 AAATTAT
78261 AAATTAT
1 AAATTAT
78268 AAATTAT
1 AAATTAT
78275 AAA
1 AAA
78278 AATATTTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (7 bp):
AAATTAT
Found at i:78542 original size:29 final size:29
Alignment explanation
Indices: 78496--78585 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 29
78486 ATCTTATGTT
*
78496 GGGGGAGAACTT-GAATTTATAAAATTCTA
1 GGGGGTGAACTTAG-ATTTATAAAATTCTA
78525 GGGGGTGAACTTAGATTTATAAAATTCTA
1 GGGGGTGAACTTAGATTTATAAAATTCTA
** *
78554 -GAAGTGAACTTAGACTTATAAAATTCTA
1 GGGGGTGAACTTAGATTTATAAAATTCTA
78582 GGGG
1 GGGG
78586 CAAATTTTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 25 0.47
29 27 0.51
30 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (29 bp):
GGGGGTGAACTTAGATTTATAAAATTCTA
Found at i:78572 original size:28 final size:28
Alignment explanation
Indices: 78512--78582 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
78502 GAACTTGAAT
** *
78512 TTATAAAATTCTAGGGGGTGAACTTAGAT
1 TTATAAAATTCTA-GAAGTGAACTTAGAC
78541 TTATAAAATTCTAGAAGTGAACTTAGAC
1 TTATAAAATTCTAGAAGTGAACTTAGAC
78569 TTATAAAATTCTAG
1 TTATAAAATTCTAG
78583 GGGCAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 26 0.67
29 13 0.33
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (28 bp):
TTATAAAATTCTAGAAGTGAACTTAGAC
Found at i:79269 original size:21 final size:20
Alignment explanation
Indices: 79245--79301 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
79235 TTTATTTTTG
79245 TAGTATTTTAATATTTATTAT
1 TAGTATTTTAATATTTATT-T
*
79266 TAGTATTTTACAT-TTAATTT
1 TAGTATTTTA-ATATTTATTT
* *
79286 TAATATTTTTATATTT
1 TAGTATTTTAATATTT
79302 TTAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.07
20 11 0.37
21 15 0.50
22 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (20 bp):
TAGTATTTTAATATTTATTT
Found at i:80892 original size:16 final size:16
Alignment explanation
Indices: 80871--80901 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
80861 AAAATTGAAA
80871 TGTAATGCATATATTC
1 TGTAATGCATATATTC
*
80887 TGTAATGTATATATT
1 TGTAATGCATATATT
80902 TTTTGATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (16 bp):
TGTAATGCATATATTC
Found at i:82685 original size:216 final size:208
Alignment explanation
Indices: 82264--82690 Score: 730
Period size: 216 Copynumber: 2.0 Consensus size: 208
82254 GCCCAAATGA
82264 TGTCTAGTATGAAAAGTATGGGAACATATAATATCAATATTATGATGTTTGTGGTTGTGATCCTT
1 TGTCTAGTATGAAAAGTATGGGAACA-ATAATATCAATATTATGATGTTTGTGGTTGTGATCCTT
82329 GACCCGAGGCACAAGTTAAATTATGTTATTGGATTGTGCAGATCTTATGATGAAACAAAAGCCAC
65 GACCCGAGGCACAAGTTAAATTATGTTATTGGATTGTGCAGATCTTATGATGAAACAAAAGCCAC
82394 TCTTTTGCTTCAAAATTAAGATGGTTTTGCAATCTTTATTTGACTCATATGCTTCTTCAATGTCT
130 TCTTTTGCTTCAAAATTAAGATGGTTTTGCAATCTTTATTTGACTCATATGCTTCTTCAATGTCT
82459 CCTTCAAAGACAAG
195 CCTTCAAAGACAAG
82473 TGTCTAAGTATGAAAAGTATTATGGGAAC-ATAATATCAATATTATGATGTTTGTGGTTGTGATC
1 TGTCT-AGTATGAAAAG---TATGGGAACAATAATATCAATATTATGATGTTTGTGGTTGTGATC
* *
82537 CTTGACCCTAGGCACAAGTTAAATTATGTTAATTGGATTTTGCATGATTCTTATGATGAAACAAA
62 CTTGACCCGAGGCACAAGTTAAATTATGTT-ATTGGATTGTGCA-GA-TCTTATGATGAAACAAA
*
82602 AGCCACTCTTTTGTGCTTTAAAATTAAGATGGTTTTGCAATCTTTATTTGACTCATATGCTTCTT
124 AGCCACTC-TTT-TGCTTCAAAATTAAGATGGTTTTGCAATCTTTATTTGACTCATATGCTTCTT
82667 CAATGTCTCCTTCAAAGACAAG
187 CAATGTCTCCTTCAAAGACAAG
82689 TG
1 TG
82691 ATATGTATTC
Statistics
Matches: 206, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
209 5 0.02
210 11 0.05
211 64 0.31
212 12 0.06
213 11 0.05
214 25 0.12
215 3 0.01
216 75 0.36
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (208 bp):
TGTCTAGTATGAAAAGTATGGGAACAATAATATCAATATTATGATGTTTGTGGTTGTGATCCTTG
ACCCGAGGCACAAGTTAAATTATGTTATTGGATTGTGCAGATCTTATGATGAAACAAAAGCCACT
CTTTTGCTTCAAAATTAAGATGGTTTTGCAATCTTTATTTGACTCATATGCTTCTTCAATGTCTC
CTTCAAAGACAAG
Found at i:83477 original size:65 final size:65
Alignment explanation
Indices: 83371--83503 Score: 196
Period size: 65 Copynumber: 2.0 Consensus size: 65
83361 TTACTATCTC
* *
83371 TTTTATTATGTTGTTAAGACTTGATACTCTTGTGTGGTA-TTTTATTTTGAACGTCTTGTGTTTG
1 TTTTATTATGTTGTTAAGACTTGATACTCTTGTGTGGTATTTTTAATTTGAACATCTTGTG-TTG
83435 A
65 A
* * * *
83436 TTTTATTGTGTTGTTGAGATTTGATACTCTTGTGTGTTATTTTTAATTTGAACATCTTGTGTTGA
1 TTTTATTATGTTGTTAAGACTTGATACTCTTGTGTGGTATTTTTAATTTGAACATCTTGTGTTGA
83501 TTT
1 TTT
83504 GAAACTTGAC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 42 0.69
66 19 0.31
ACGTcount: A:0.18, C:0.07, G:0.20, T:0.56
Consensus pattern (65 bp):
TTTTATTATGTTGTTAAGACTTGATACTCTTGTGTGGTATTTTTAATTTGAACATCTTGTGTTGA
Found at i:90402 original size:46 final size:46
Alignment explanation
Indices: 90258--90404 Score: 222
Period size: 46 Copynumber: 3.2 Consensus size: 46
90248 TTTTCGTGTG
* * *
90258 CGACATTCATCAGTGGTGTGTTTTGGAATAAATGTGTTTCAATATT
1 CGACGTTCATTAGTGGTGTGTTTTGGAATAAATGTGTTTCAATATA
* **
90304 CGACGTTCATTAGTGGTGTGTTTTGGAATAAATGTCTTTTGATATA
1 CGACGTTCATTAGTGGTGTGTTTTGGAATAAATGTGTTTCAATATA
* *
90350 CTACGTTCATTAGTGGTGTGTTTTGGAATAAATGTGTTTCAATACA
1 CGACGTTCATTAGTGGTGTGTTTTGGAATAAATGTGTTTCAATATA
90396 CGACGTTCA
1 CGACGTTCA
90405 CTGTAGACGC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 89 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (46 bp):
CGACGTTCATTAGTGGTGTGTTTTGGAATAAATGTGTTTCAATATA
Found at i:91479 original size:31 final size:31
Alignment explanation
Indices: 91442--91515 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
91432 TGTACAAAAT
* * *
91442 ACATCATATATTTAATCAACCAGAACATATA
1 ACATCATACATTTAACCAACAAGAACATATA
* *
91473 TCATCATGCATTTAACCAACAAGAACATATA
1 ACATCATACATTTAACCAACAAGAACATATA
*
91504 ACATCATGCATT
1 ACATCATACATT
91516 GATCATTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.45, C:0.22, G:0.05, T:0.28
Consensus pattern (31 bp):
ACATCATACATTTAACCAACAAGAACATATA
Found at i:91651 original size:24 final size:22
Alignment explanation
Indices: 91617--91660 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
91607 CACTACAACT
*
91617 CGTAAAATGCATCGAAGTGCAG
1 CGTAAAATGCACCGAAGTGCAG
91639 CGTAGAAATTGCACCGAAGTGC
1 CGTA-AAA-TGCACCGAAGTGC
91661 CACATAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.18
Consensus pattern (22 bp):
CGTAAAATGCACCGAAGTGCAG
Found at i:91668 original size:24 final size:24
Alignment explanation
Indices: 91624--91671 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
91614 ACTCGTAAAA
* *
91624 TGCATCGAAGTGCAGCGTAGAAAT
1 TGCACCGAAGTGCAGCATAGAAAT
91648 TGCACCGAAGTGCCA-CATAGAAAT
1 TGCACCGAAGTG-CAGCATAGAAAT
91672 ATCCCAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (24 bp):
TGCACCGAAGTGCAGCATAGAAAT
Found at i:91689 original size:23 final size:23
Alignment explanation
Indices: 91660--91752 Score: 69
Period size: 23 Copynumber: 4.0 Consensus size: 23
91650 CACCGAAGTG
91660 CCACATAGAAATATCCCAAAGGA
1 CCACATAGAAATATCCCAAAGGA
* * * * **
91683 CCACATAGTATTGTCCAAAAATA
1 CCACATAGAAATATCCCAAAGGA
* * *
91706 CCACGTAAAAATATCCCGAAGGA
1 CCACATAGAAATATCCCAAAGGA
* * * *
91729 CCACGTAGAATTGTCCCGAAGGA
1 CCACATAGAAATATCCCAAAGGA
91752 C
1 C
91753 TGCGTAGAAC
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.17
Consensus pattern (23 bp):
CCACATAGAAATATCCCAAAGGA
Found at i:92746 original size:18 final size:20
Alignment explanation
Indices: 92718--92754 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
92708 TTCAGTACTT
92718 CAAACTCAAC-TATATCACC
1 CAAACTCAACTTATATCACC
92737 CAAA-TCAACTTATATCAC
1 CAAACTCAACTTATATCAC
92755 TTTAACACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.24
Consensus pattern (20 bp):
CAAACTCAACTTATATCACC
Done.