Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007080.1 Hibiscus syriacus cultivar Beakdansim tig00018477_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: 94650
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7711 original size:15 final size:15
Alignment explanation
Indices: 7691--7723 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
7681 ATCAACAGAT
7691 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
7706 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
7721 ATA
1 ATA
7724 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:21100 original size:45 final size:45
Alignment explanation
Indices: 21051--21138 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
21041 AAAATAGCCA
* *
21051 GAGTGCATCGATGCATAGCT-TGCGCATCGATCCATCAAATGCACT
1 GAGTGCATCAATGCAT-GCTATGCGCATCGATCCATAAAATGCACT
* * *
21096 GAGTGCATCAATGCATGGTATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCAATGCATGCTATGCGCATCGATCCATAAAATGCA
21139 TTCGATGTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (45 bp):
GAGTGCATCAATGCATGCTATGCGCATCGATCCATAAAATGCACT
Found at i:22256 original size:21 final size:21
Alignment explanation
Indices: 22222--22265 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22212 CCGGAGGAGG
* *
22222 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
*
22243 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
22264 AG
1 AG
22266 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.39, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:23866 original size:21 final size:22
Alignment explanation
Indices: 23805--23885 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
23795 CATGGCCTTG
23805 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
* * * *
23828 TGCATCGGTGTACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
23849 TGTATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AA-GGA
*
23873 TACATCGATGCAC
1 TGCATCGATGCAC
23886 TGTTAAGTGT
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
21 13 0.30
22 1 0.02
23 19 0.43
24 11 0.25
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:25659 original size:21 final size:21
Alignment explanation
Indices: 25633--25677 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25623 GATTTCTGGG
* *
25633 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
25654 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
25675 CAA
1 CAA
25678 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:26049 original size:24 final size:22
Alignment explanation
Indices: 26022--26066 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
26012 TATATGATTG
26022 TATGATTATGTTTATATTACATGA
1 TATGATTA-G-TTATATTACATGA
* *
26046 TATGTTTAGTTGTATTACATG
1 TATGATTAGTTATATTACATG
26067 TTAGGTGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (22 bp):
TATGATTAGTTATATTACATGA
Found at i:26160 original size:2 final size:2
Alignment explanation
Indices: 26153--26189 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
26143 CATGAGTTAG
26153 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26190 GGAATTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27066 original size:32 final size:31
Alignment explanation
Indices: 27024--27124 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
27014 AGAGTCGAGG
27024 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
27055 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
27087 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
27118 ATTTACC
1 GTTTACC
27125 GAGGATCTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
31 31 0.53
32 28 0.47
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:27155 original size:30 final size:30
Alignment explanation
Indices: 27120--27205 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
27110 TATGGACAAT
27120 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
*
27150 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
* * *
27180 TTACCG-GGGTCTGTGTGACCTCTGGA
1 TTACCGAGGATCTTTATGACCTCTGGA
27206 TAGGTCCTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 17 0.33
30 35 0.67
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGACAG
Found at i:33141 original size:37 final size:37
Alignment explanation
Indices: 33091--33166 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
33081 GATCGAAAAG
* *
33091 CTAAACAAAGCAATGCCCTTAGTCGAGGGATTATGTA
1 CTAAACAAAGCAATGCCCTTAGTCGAGAGACTATGTA
*
33128 CTAAAGAAAGCAATGCCCTTAGTCGAGAGACTATGTA
1 CTAAACAAAGCAATGCCCTTAGTCGAGAGACTATGTA
33165 CT
1 CT
33167 CAATAAGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (37 bp):
CTAAACAAAGCAATGCCCTTAGTCGAGAGACTATGTA
Found at i:39913 original size:23 final size:23
Alignment explanation
Indices: 39883--39932 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
39873 ATACTTTACA
*
39883 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATC
39906 ATATAAGCACTACCTATTACATC
1 ATATAAGCACTACCTATTACATC
39929 ATAT
1 ATAT
39933 TTTTACCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATC
Found at i:41402 original size:60 final size:60
Alignment explanation
Indices: 41289--41402 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
41279 AATAGTGGGG
* * * * * **
41289 TGACCATTTTCTAACTTTTAATAATCTAGGGACTTAACAAATCAACATTCTATAATCGAA
1 TGACCATTTTATAAATTTTAATAACCGAGGGACTTAACAAAGCAACACCCTATAATCGAA
* * *
41349 TGACGATTTTATAAATTTTAATAACCGAGGGACTTAATAAAGCAATACCCTATA
1 TGACCATTTTATAAATTTTAATAACCGAGGGACTTAACAAAGCAACACCCTATA
41403 GACATGAGAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (60 bp):
TGACCATTTTATAAATTTTAATAACCGAGGGACTTAACAAAGCAACACCCTATAATCGAA
Found at i:44427 original size:2 final size:2
Alignment explanation
Indices: 44420--44458 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
44410 CACGCACTCC
44420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44459 CTGTTCGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47786 original size:23 final size:22
Alignment explanation
Indices: 47759--47808 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
47749 CCAAACGACA
47759 AAAAAACGTG-TCATAAAGGTAG
1 AAAAAACGTGCT-ATAAAGGTAG
*
47781 AGAAAAACTTGCTATAAAGGTAG
1 A-AAAAACGTGCTATAAAGGTAG
47804 AAAAA
1 AAAAA
47809 GACCATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 19 0.76
24 1 0.04
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.18
Consensus pattern (22 bp):
AAAAAACGTGCTATAAAGGTAG
Found at i:48942 original size:31 final size:29
Alignment explanation
Indices: 48907--48965 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
48897 GTTGGTGGCT
*
48907 TGATTAACATCATTTAAATAGTTAAGTGGTA
1 TGATTAACA-CAATTAAA-AGTTAAGTGGTA
* *
48938 TGATTGACACAATTAAAAGTTGAGTGGT
1 TGATTAACACAATTAAAAGTTAAGTGGT
48966 CGGATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 7 0.28
31 8 0.32
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (29 bp):
TGATTAACACAATTAAAAGTTAAGTGGTA
Found at i:52935 original size:36 final size:38
Alignment explanation
Indices: 52895--52970 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 38
52885 ACTTAGCGTT
52895 AAGTTTTGAACG-GA-TACTAAAATGAAACAAAAACTA
1 AAGTTTTGAACGAGAGTACTAAAATGAAACAAAAACTA
* * *
52931 AAGTTTTTAATGACGATGTACTAAAATGAAACACAAACTA
1 AAGTTTTGAACGA-GA-GTACTAAAATGAAACAAAAACTA
52971 CACTATAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 10 0.30
38 2 0.06
40 21 0.64
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (38 bp):
AAGTTTTGAACGAGAGTACTAAAATGAAACAAAAACTA
Found at i:53177 original size:16 final size:16
Alignment explanation
Indices: 53156--53235 Score: 78
Period size: 16 Copynumber: 5.1 Consensus size: 16
53146 AAAAAAGCAA
53156 TTTATTCACTGAATTT
1 TTTATTCACTGAATTT
*
53172 TTTATTTACT--ATTAT
1 TTTATTCACTGAATT-T
*
53187 TTTAGTCACTGAATTT
1 TTTATTCACTGAATTT
*
53203 TTTATTTACT--ATTAT
1 TTTATTCACTGAATT-T
*
53218 TTTAGTCACTGAATTT
1 TTTATTCACTGAATTT
53234 TT
1 TT
53236 AAAAAAATTG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.12
15 18 0.35
16 21 0.41
17 6 0.12
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTATTCACTGAATTT
Found at i:53196 original size:31 final size:31
Alignment explanation
Indices: 53156--53235 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
53146 AAAAAAGCAA
*
53156 TTTATTCACTGAATTTTTTATTTACTATTAT
1 TTTAGTCACTGAATTTTTTATTTACTATTAT
53187 TTTAGTCACTGAATTTTTTATTTACTATTAT
1 TTTAGTCACTGAATTTTTTATTTACTATTAT
53218 TTTAGTCACTGAATTTTT
1 TTTAGTCACTGAATTTTT
53236 AAAAAAATTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.59
Consensus pattern (31 bp):
TTTAGTCACTGAATTTTTTATTTACTATTAT
Found at i:53204 original size:15 final size:15
Alignment explanation
Indices: 53186--53236 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
53176 TTTACTATTA
53186 TTTTAGTCACTGAATT
1 TTTTAGTCACTGAA-T
* * *
53202 TTTTATTTACT-ATT
1 TTTTAGTCACTGAAT
53216 ATTTTAGTCACTGAAT
1 -TTTTAGTCACTGAAT
53232 TTTTA
1 TTTTA
53237 AAAAAATTGC
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
14 1 0.04
15 15 0.56
16 11 0.41
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (15 bp):
TTTTAGTCACTGAAT
Found at i:53787 original size:13 final size:13
Alignment explanation
Indices: 53754--53789 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
53744 TTAATTAGGT
53754 TTCTATATT-TTA
1 TTCTATATTATTA
53766 TT-TAT-TTATTA
1 TTCTATATTATTA
53777 TTCTATATTATTA
1 TTCTATATTATTA
53790 ATTAATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.10
11 8 0.38
12 5 0.24
13 6 0.29
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (13 bp):
TTCTATATTATTA
Found at i:53797 original size:21 final size:22
Alignment explanation
Indices: 53754--53797 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
53744 TTAATTAGGT
* *
53754 TTCTATATTTTATTTATTTATTA
1 TTCTATA-TTTATTAATTAATTA
53777 TTCTATA-TTATTAATTAATTA
1 TTCTATATTTATTAATTAATTA
53798 GATATTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (22 bp):
TTCTATATTTATTAATTAATTA
Found at i:54527 original size:6 final size:7
Alignment explanation
Indices: 54512--54538 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
54502 AATATGTAAC
54512 TTTTATT
1 TTTTATT
54519 TTTTATT
1 TTTTATT
54526 TTTTATT
1 TTTTATT
54533 TTTTAT
1 TTTTAT
54539 CATACTATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:56804 original size:30 final size:31
Alignment explanation
Indices: 56751--56809 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
56741 AATAAATTGC
56751 ATTTTATTTTTATCTTAAATTTTAAAATATT
1 ATTTTATTTTTATCTTAAATTTTAAAATATT
56782 ATTTTATTTTTATCTT-AATTTTAAAATA
1 ATTTTATTTTTATCTTAAATTTTAAAATA
56810 GTATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
ATTTTATTTTTATCTTAAATTTTAAAATATT
Found at i:56862 original size:38 final size:38
Alignment explanation
Indices: 56789--56879 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
56779 ATTATTTTAT
56789 TTTTATCTTAATTTTAAAATAGTATAATAATAAAATATA
1 TTTTATCTTAA-TTTAAAATAGTATAATAATAAAATATA
* * * * *
56828 TTTTCTCTTAATTTAAAATATTTTAAT-TTAAAAATGTA
1 TTTTATCTTAATTTAAAATAGTATAATAAT-AAAATATA
*
56866 TTTTATTTTAATTT
1 TTTTATCTTAATTT
56880 TAATTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 1 0.02
38 33 0.75
39 10 0.23
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (38 bp):
TTTTATCTTAATTTAAAATAGTATAATAATAAAATATA
Found at i:56869 original size:18 final size:16
Alignment explanation
Indices: 56835--56876 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
56825 ATATTTTCTC
56835 TTAATTT-AAAATATT
1 TTAATTTAAAAATATT
56850 TTAATTTAAAAATGTATT
1 TTAATTTAAAAA--TATT
*
56868 TTATTTTAA
1 TTAATTTAA
56877 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
18 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTAATTTAAAAATATT
Found at i:56933 original size:20 final size:21
Alignment explanation
Indices: 56888--56928 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
56878 TTTAATTTTA
56888 AAATATTATAAGATTAAAAGT
1 AAATATTATAAGATTAAAAGT
56909 AAATATT-TAAG-TT-AAAGT
1 AAATATTATAAGATTAAAAGT
56927 AA
1 AA
56929 GAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 4 0.20
21 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (21 bp):
AAATATTATAAGATTAAAAGT
Found at i:61638 original size:19 final size:19
Alignment explanation
Indices: 61581--61638 Score: 75
Period size: 17 Copynumber: 3.1 Consensus size: 19
61571 TTAGAGATAT
*
61581 TTTATAGTAATAATTCTAAA
1 TTTATA-TAATAATTTTAAA
61601 TTTATATAAT-ATTTT-AA
1 TTTATATAATAATTTTAAA
*
61618 TTTTTATAATAATTTTAAA
1 TTTATATAATAATTTTAAA
61637 TT
1 TT
61639 GGGTAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 11 0.32
18 9 0.26
19 8 0.24
20 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTATATAATAATTTTAAA
Found at i:62125 original size:25 final size:25
Alignment explanation
Indices: 62073--62125 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
62063 ATTATGTATG
* *
62073 AATTTTTAAATTTTTAAAATAATTA
1 AATTTTTAAATTTTAAAAATAATAA
62098 AATTTATTAAATTTTAAAAATAA-AA
1 AATTT-TTAAATTTTAAAAATAATAA
62123 AAT
1 AAT
62126 AAATTATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTTTTAAATTTTAAAAATAATAA
Found at i:62131 original size:25 final size:26
Alignment explanation
Indices: 62078--62131 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
62068 GTATGAATTT
* * **
62078 TTAAATTTTTAAAATAATTAAATTTA
1 TTAAATTTTAAAAATAATAAAATAAA
62104 TTAAATTTTAAAAATAA-AAAATAAA
1 TTAAATTTTAAAAATAATAAAATAAA
62129 TTA
1 TTA
62132 TCAATTGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TTAAATTTTAAAAATAATAAAATAAA
Found at i:69606 original size:19 final size:19
Alignment explanation
Indices: 69582--69620 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
69572 TCGAATGCAT
69582 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
69601 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
69620 T
1 T
69621 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:69637 original size:65 final size:63
Alignment explanation
Indices: 69519--69727 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
69509 TATTCAAAGG
* *
69519 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
69581 TTC
61 TTT
69584 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
69649 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTT
*
69713 CATGCATCGATGCAC
1 CATGCACCGATGCAC
69728 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 53 0.42
65 64 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:69721 original size:64 final size:65
Alignment explanation
Indices: 69568--69728 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
69558 GAATTAATTG
* * *** *
69568 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
69633 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
69696 A
65 A
69697 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
69729 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:69743 original size:64 final size:64
Alignment explanation
Indices: 69519--69748 Score: 225
Period size: 64 Copynumber: 3.6 Consensus size: 64
69509 TATTCAAAGG
* * * *
69519 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
69581 TTC
62 TTT
* * *
69584 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
69649 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
69713 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
69749 AGTGTTCCAA
Statistics
Matches: 139, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 69 0.50
65 64 0.46
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:75546 original size:20 final size:21
Alignment explanation
Indices: 75517--75572 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
75507 TTTGTGCTTC
*
75517 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
75537 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
75559 ATGCATCGATGCAT
1 ATGCATCGATGCAT
75573 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:77146 original size:21 final size:21
Alignment explanation
Indices: 77104--77147 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
77094 ACCCCGGGAG
*
77104 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
77125 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
77146 CT
1 CT
77148 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:78152 original size:8 final size:8
Alignment explanation
Indices: 78141--78167 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
78131 GCATCAGTCC
78141 ATGCATCG
1 ATGCATCG
78149 ATGCATCG
1 ATGCATCG
78157 ATGCATCG
1 ATGCATCG
78165 ATG
1 ATG
78168 AATTAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (8 bp):
ATGCATCG
Found at i:78215 original size:19 final size:19
Alignment explanation
Indices: 78191--78229 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
78181 TCGAATGCAT
78191 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
78210 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
78229 T
1 T
78230 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:78217 original size:64 final size:64
Alignment explanation
Indices: 78149--78337 Score: 215
Period size: 65 Copynumber: 2.9 Consensus size: 64
78139 CCATGCATCG
* * * * ***
78149 ATGCATCGATGCATCGATGAATTAATT-GAACATCGAATGCATTCCATGCACCGATGCACTCTCC
1 ATGCATCGATGCATC-ATGAATTATTTCAAACATCGAATGCATTTCATGCATCGATGCACAAGCC
*
78213 ATGCATCGATGCACTC-TGAA-TATTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAAG
1 ATGCATCGATGCA-TCATGAATTA-TTTC-AAACATCGAATGCATTTCATGCATCGATGCACAAG
78276 CC
63 CC
* *
78278 ATGCATCGATGCATCAGGCTATT-TTTCAAACATCGAATGCATTTCATGCATCGATGCACA
1 ATGCATCGATGCATCATG-AATTATTTCAAACATCGAATGCATTTCATGCATCGATGCACA
78338 CTTGGTGCAC
Statistics
Matches: 107, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
62 2 0.02
63 6 0.06
64 47 0.44
65 50 0.47
66 1 0.01
67 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCATCATGAATTATTTCAAACATCGAATGCATTTCATGCATCGATGCACAAGCC
Found at i:78253 original size:65 final size:64
Alignment explanation
Indices: 78177--78337 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 64
78167 GAATTAATTG
* * *** *
78177 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGAATATTTTTC-
78241 A
64 A
* **
78242 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCA
78306 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
78338 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCA
Found at i:78352 original size:64 final size:64
Alignment explanation
Indices: 78177--78357 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
78167 GAATTAATTG
* * * *
78177 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
78242 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
78306 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
78358 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 48 0.48
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:80218 original size:17 final size:17
Alignment explanation
Indices: 80196--80229 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
80186 ACAATTATTT
80196 TAAATAATATCTAATTA
1 TAAATAATATCTAATTA
80213 TAAATAATATCTAATTA
1 TAAATAATATCTAATTA
80230 ATTTGATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATAATATCTAATTA
Found at i:83189 original size:26 final size:26
Alignment explanation
Indices: 83149--83205 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
83139 ACACGTCTGA
83149 GCGCCTCCACATCTTGGCCGACGCGG
1 GCGCCTCCACATCTTGGCCGACGCGG
*
83175 GCGCCTCCACCTCTTGGCCGACGCGG
1 GCGCCTCCACATCTTGGCCGACGCGG
83201 GCGCC
1 GCGCC
83206 GATGGAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.09, C:0.46, G:0.32, T:0.14
Consensus pattern (26 bp):
GCGCCTCCACATCTTGGCCGACGCGG
Found at i:92941 original size:16 final size:16
Alignment explanation
Indices: 92920--92954 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
92910 TTTTTTTAAG
92920 GATTATGTTGGGTCGA
1 GATTATGTTGGGTCGA
92936 GATTATGTTGGGTCGA
1 GATTATGTTGGGTCGA
92952 GAT
1 GAT
92955 CGAGTTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.06, G:0.37, T:0.37
Consensus pattern (16 bp):
GATTATGTTGGGTCGA
Done.