Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005125.1 Hibiscus syriacus cultivar Beakdansim tig00011526_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: 92500
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6089 original size:15 final size:15
Alignment explanation
Indices: 6069--6101 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6059 AGAACAAGGT
6069 CCCTGAGCCCTAGGC
1 CCCTGAGCCCTAGGC
6084 CCCTGAGCCCTAGGC
1 CCCTGAGCCCTAGGC
6099 CCC
1 CCC
6102 CTCTGATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.52, G:0.24, T:0.12
Consensus pattern (15 bp):
CCCTGAGCCCTAGGC
Found at i:13894 original size:34 final size:34
Alignment explanation
Indices: 13855--13923 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
13845 AAAAACTGAA
*
13855 AGAGCATGCAAAAAGATGACTTAAAAAGTCTAGT
1 AGAGCATACAAAAAGATGACTTAAAAAGTCTAGT
13889 AGAGCATACAAAAAGATGACTTAAAAAGTCTAGT
1 AGAGCATACAAAAAGATGACTTAAAAAGTCTAGT
13923 A
1 A
13924 TCATCGGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (34 bp):
AGAGCATACAAAAAGATGACTTAAAAAGTCTAGT
Found at i:19585 original size:14 final size:14
Alignment explanation
Indices: 19566--19592 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19556 TAGAATTATT
19566 TTAGTTTATTTTAC
1 TTAGTTTATTTTAC
19580 TTAGTTTATTTTA
1 TTAGTTTATTTTA
19593 TTGATAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (14 bp):
TTAGTTTATTTTAC
Found at i:27514 original size:18 final size:17
Alignment explanation
Indices: 27491--27524 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27481 CAGTCTGTGT
27491 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
27509 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
27525 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:27941 original size:26 final size:25
Alignment explanation
Indices: 27892--27941 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
27882 TTTAGTAAAA
* * *
27892 TTATTGAATAAATAATGAATTTATT
1 TTATTGAATAAAGAAAGAAATTATT
27917 TTATTGTAATAAAGAAAGAAATTAT
1 TTATTG-AATAAAGAAAGAAATTAT
27942 AATATGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (25 bp):
TTATTGAATAAAGAAAGAAATTATT
Found at i:31487 original size:15 final size:15
Alignment explanation
Indices: 31439--31488 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
31429 TCAACCAACC
31439 AAATAATAATATATTT
1 AAATAATAATATA-TT
* * *
31455 ATAATCACAATCTATT
1 A-AATAATAATATATT
31471 AAATAATAATATATT
1 AAATAATAATATATT
31486 AAA
1 AAA
31489 CCAACCATGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 14 0.52
16 4 0.15
17 9 0.33
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAATAATATATT
Found at i:34607 original size:60 final size:60
Alignment explanation
Indices: 34511--34627 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
34501 TAAAGTATAC
* * * **
34511 AAATGGTCCCTCAACTATATGGTTTTGCTTTATTGAGTCATTCGACTATTAAAAGTTATG
1 AAATGGTCCCTCAACTATAGGGTATTACTTTATTGAGTCACCCGACTATTAAAAGTTATG
** * * *
34571 AAATGGTCCCTTGATTATAGGGTATTACTTTGTTGAGTCCCCCGACTATTAAAAGTT
1 AAATGGTCCCTCAACTATAGGGTATTACTTTATTGAGTCACCCGACTATTAAAAGTT
34628 GCAAAATGGT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (60 bp):
AAATGGTCCCTCAACTATAGGGTATTACTTTATTGAGTCACCCGACTATTAAAAGTTATG
Found at i:34934 original size:60 final size:60
Alignment explanation
Indices: 34841--34978 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 60
34831 GAACATATGA
* * * ** **
34841 ATAGTCGGGTGACCATTTTATAACTTTTGATAGTCGATG-GACTCAACAAAGTAACGTCCT
1 ATAGTTGGGGGACCATTTTATAACTTTTAATAGTC-ATGAGACTCAACAAAACAACACCCT
* * *
34901 ATAGTTGGGGGACTATTTTGTAACTTTTAATAGTCATGAGACTCAATAAAACAACACCCT
1 ATAGTTGGGGGACCATTTTATAACTTTTAATAGTCATGAGACTCAACAAAACAACACCCT
34961 ATAGTTGGGGGACCATTT
1 ATAGTTGGGGGACCATTT
34979 GTATTCTTTA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 3 0.05
60 63 0.95
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (60 bp):
ATAGTTGGGGGACCATTTTATAACTTTTAATAGTCATGAGACTCAACAAAACAACACCCT
Found at i:35070 original size:20 final size:21
Alignment explanation
Indices: 35040--35080 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
35030 AAAAATTTAA
*
35040 AAAATATATAATAATTAAATT
1 AAAATATATAAAAATTAAATT
35061 AAAA-ATATAAAAATTAAATT
1 AAAATATATAAAAATTAAATT
35081 CGTAACTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATATATAAAAATTAAATT
Found at i:43252 original size:15 final size:15
Alignment explanation
Indices: 43232--43260 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43222 CAGGTGAAAA
43232 TATTACTTTATTAGC
1 TATTACTTTATTAGC
43247 TATTACTTTATTAG
1 TATTACTTTATTAG
43261 GAGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (15 bp):
TATTACTTTATTAGC
Found at i:45487 original size:15 final size:16
Alignment explanation
Indices: 45458--45489 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
45448 ATGAAAAAAT
45458 TGATATAATTTTTAAA
1 TGATATAATTTTTAAA
45474 TGATATAA-TTTTAAA
1 TGATATAATTTTTAAA
45489 T
1 T
45490 ATCAAAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TGATATAATTTTTAAA
Found at i:47850 original size:16 final size:17
Alignment explanation
Indices: 47829--47881 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 17
47819 TTTTAAATTT
47829 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
47845 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
47860 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
47877 AATTA
1 AATTA
47882 TTTTATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 7 0.23
17 7 0.23
18 3 0.10
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:55177 original size:22 final size:22
Alignment explanation
Indices: 55160--55226 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
55150 CTCGTATAAA
55160 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
55182 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
55204 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
55226 T
1 T
55227 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:55487 original size:30 final size:31
Alignment explanation
Indices: 55446--55505 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
55436 TAGCCATAGT
*
55446 ATTTTCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
55476 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
55506 AACGTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:55562 original size:29 final size:28
Alignment explanation
Indices: 55520--55590 Score: 106
Period size: 29 Copynumber: 2.5 Consensus size: 28
55510 TTTTCTGCAT
*
55520 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATA-CA
* *
55549 ATTCATGTCATGTAATACCTTTAATACA
1 ATTCATGTCATGTAATACATATAATACA
55577 ATTCATGTCATGTA
1 ATTCATGTCATGTA
55591 TCATAATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 15 0.38
29 24 0.62
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATACA
Found at i:56009 original size:66 final size:66
Alignment explanation
Indices: 55892--56063 Score: 186
Period size: 66 Copynumber: 2.6 Consensus size: 66
55882 CTTTTCTCAT
* * * *
55892 GGGGGAATCGGTTCCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCTTATACGA
1 GGGGGTATCGGTT-CCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAA-ATCATATACGA
55957 TGA
64 TGA
* * * * *
55960 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATT-CCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGGTATCGGTTCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
56024 A
66 A
* * *
56025 AGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCT--AGGGGTACCGATTCCCCT
56064 AACCCAGAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
64 5 0.06
65 22 0.25
66 27 0.31
67 22 0.25
68 12 0.14
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.28
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
A
Found at i:56051 original size:21 final size:21
Alignment explanation
Indices: 56021--56063 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56011 ATCATATTCG
* *
56021 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
56042 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
56063 T
1 T
56064 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:62110 original size:22 final size:22
Alignment explanation
Indices: 62093--62159 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
62083 CTCGTATAAA
62093 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
62115 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
62137 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
62159 T
1 T
62160 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:62418 original size:30 final size:31
Alignment explanation
Indices: 62377--62436 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
62367 TAGCCATAGT
*
62377 ATTTTCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
62407 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
62437 AACGTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:62493 original size:29 final size:29
Alignment explanation
Indices: 62451--62522 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
62441 TTTTCTGCAT
**
62451 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
* *
62480 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
62509 ATTCATGTCATGTA
1 ATTCATGTCATGTA
62523 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:62920 original size:68 final size:67
Alignment explanation
Indices: 62825--62976 Score: 205
Period size: 68 Copynumber: 2.3 Consensus size: 67
62815 TTTTTCTCAT
* * * *
62825 GGGGGAATCGGTTCCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCTTATACGA
1 GGGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAA-ATCATATACGA
62890 TGA
65 TGA
* * * * *
62893 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTT
1 GGGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
62958 GA
66 GA
*
62960 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
62977 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 26 0.35
68 48 0.65
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
GA
Found at i:62986 original size:21 final size:21
Alignment explanation
Indices: 62956--62998 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
62946 ATCATATTCG
* *
62956 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
62977 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
62998 T
1 T
62999 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:62989 original size:67 final size:67
Alignment explanation
Indices: 62826--62998 Score: 188
Period size: 68 Copynumber: 2.6 Consensus size: 67
62816 TTTTCTCATG
* * * * *
62826 GGGGAATCGGTTCCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCTTATACGAT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
*
62891 GAG
65 GAA
* * * *
62894 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
62958 GAA
65 GAA
* *
62961 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
62999 AACCCAGAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 6 0.07
67 38 0.42
68 47 0.52
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATG
AA
Found at i:64991 original size:16 final size:16
Alignment explanation
Indices: 64970--65003 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
64960 TCAAATAATC
64970 ATATA-TAAAAAATATT
1 ATATATTAAAAAA-ATT
64986 ATATATTAAAAAAATT
1 ATATATTAAAAAAATT
65002 AT
1 AT
65004 CTTATAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATATTAAAAAAATT
Found at i:65840 original size:16 final size:16
Alignment explanation
Indices: 65821--65861 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
65811 TTATTTATTA
65821 ATTTTTATAAAAAAAT
1 ATTTTTATAAAAAAAT
*
65837 A-TTTT-TAATAAAAT
1 ATTTTTATAAAAAAAT
65851 ATTTTTA-AAAA
1 ATTTTTATAAAA
65862 TTAAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
14 9 0.43
15 11 0.52
16 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTTTATAAAAAAAT
Found at i:65851 original size:14 final size:14
Alignment explanation
Indices: 65832--65858 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65822 TTTTTATAAA
65832 AAAATATTTTTAAT
1 AAAATATTTTTAAT
65846 AAAATATTTTTAA
1 AAAATATTTTTAA
65859 AAATTAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTTTTAAT
Found at i:66743 original size:26 final size:26
Alignment explanation
Indices: 66712--66761 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
66702 TTTTCCTTCT
66712 TTTTATTTTATTGTTAGATTTTTTCA
1 TTTTATTTTATTGTTAGATTTTTTCA
66738 TTTTATTTTATTGTTAGATTTTTT
1 TTTTATTTTATTGTTAGATTTTTT
66762 TCTTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.72
Consensus pattern (26 bp):
TTTTATTTTATTGTTAGATTTTTTCA
Found at i:82952 original size:55 final size:55
Alignment explanation
Indices: 82854--82959 Score: 187
Period size: 55 Copynumber: 1.9 Consensus size: 55
82844 GCGGATTACA
82854 TATATATTTGATATCATACTATTTAATAATTAACTTTATTTTATAATAATTTATG
1 TATATATTTGATATCATACTATTTAATAATTAACTTTATTTTATAATAATTTATG
*
82909 TATATATTTGATATCATACTGTATTAATAATTAACTTTA-TTTATAATAATT
1 TATATATTTGATATCATACTAT-TTAATAATTAACTTTATTTTATAATAATT
82960 ATAAATAAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
55 33 0.67
56 16 0.33
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (55 bp):
TATATATTTGATATCATACTATTTAATAATTAACTTTATTTTATAATAATTTATG
Found at i:83463 original size:120 final size:119
Alignment explanation
Indices: 83336--83815 Score: 613
Period size: 120 Copynumber: 4.0 Consensus size: 119
83326 TAACATAAAA
* * * *
83336 ATATATATTTTATCTCATCCTAATTTTTAAAATTTAATAAAATTGATATAATTATACATTTTGTC
1 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTC
* *
83401 ACTTATACTTTTATATTTTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATATAT
66 ACTTATACTTATATATTCTATCAATTTAAAA-TAATTTTAAAAAATT-AAAAT-TAT
83458 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTC
1 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTC
* * *** *
83523 ACTTTTTCTTATATATTCTATCAATTTAGTCCTAATTTTAATAAATTAAAATTACT
66 ACTTATACTTATATATTCTATCAATTTA-AAATAATTTTAAAAAATTAAAATTA-T
* *
83579 TTATAT-TTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTC
1 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTC
* * *** *
83643 ACTTACACTTTTATATTCTATCAATTTAGTTTAATTTTAAAAAATTATAATTAAT
66 ACTTATACTTATATATTCTATCAATTTAAAATAATTTTAAAAAATTAAAATT-AT
* * * * *
83698 TTATATATTTTATCTCGTCTTAAC-TTTGAAACTTAATAAAATTGATATAATTACACATTTGATC
1 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTC
* * ** *
83762 ACTTTTACTTATATATTATATCAATTTAGTCATAATTTTAATAAATTAAAATTA
66 ACTTATACTTATATATTCTATCAATTTA-AAATAATTTTAAAAAATTAAAATTA
83816 ATTTAATCTT
Statistics
Matches: 316, Mismatches: 37, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
119 87 0.28
120 119 0.38
121 11 0.03
122 99 0.31
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.47
Consensus pattern (119 bp):
ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTC
ACTTATACTTATATATTCTATCAATTTAAAATAATTTTAAAAAATTAAAATTAT
Found at i:83811 original size:239 final size:243
Alignment explanation
Indices: 83337--83820 Score: 751
Period size: 239 Copynumber: 2.0 Consensus size: 243
83327 AACATAAAAA
* * * *
83337 TATATATTTTATCTCATCCTAATTTTTAAAATTTAATAAAATTGATATAATTATACATTTTGTCA
1 TATATATTTTATCTCATCCTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTCA
* *
83402 CTTATACTTTTATATTTTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATATATATATATATT
66 CTTACACTTTTATATTCTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATATATATATATATT
* * *
83467 TTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCACTTTTTCT
131 TTATCTCATCTTAACTTTTAAAACTTAATAAAATTGATATAATTACACATTTGATCACTTTTACT
* * *
83532 TATATATTCTATCAATTTAGTCCTAATTTTAATAAATTAAAATTACTT
196 TATATATTATATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
*
83580 TATAT-TTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTCA
1 TATATATTTTATCTCATCCTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTCA
*** * * *
83644 CTTACACTTTTATATTCTATCAATTT-AGTTTAATTTTAAAAAATTATAATTA-ATTTATATATT
66 CTTACACTTTTATATTCTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATATATATATATATT
* *
83707 TTATCTCGTCTTAAC-TTTGAAACTTAATAAAATTGATATAATTACACATTTGATCACTTTTACT
131 TTATCTCATCTTAACTTTTAAAACTTAATAAAATTGATATAATTACACATTTGATCACTTTTACT
83771 TATATATTATATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
196 TATATATTATATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
83819 TA
1 TA
83821 ATCTTTGAAT
Statistics
Matches: 220, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
239 92 0.42
240 24 0.11
241 21 0.10
242 78 0.35
243 5 0.02
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (243 bp):
TATATATTTTATCTCATCCTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTCA
CTTACACTTTTATATTCTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATATATATATATATT
TTATCTCATCTTAACTTTTAAAACTTAATAAAATTGATATAATTACACATTTGATCACTTTTACT
TATATATTATATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
Found at i:86165 original size:18 final size:18
Alignment explanation
Indices: 86144--86189 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
86134 TCTACCATTT
*
86144 AATAATAAT-TTATTCTCA
1 AATAATAATATT-TTATCA
*
86162 AATAATAATATTTTATTA
1 AATAATAATATTTTATCA
86180 AATAATAATA
1 AATAATAATA
86190 ACACCATCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAATAATATTTTATCA
Found at i:86167 original size:21 final size:18
Alignment explanation
Indices: 86143--86190 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
86133 TTCTACCATT
86143 TAATAATAATTTATTCTCAAA
1 TAATAATAATTTA-T-T-AAA
*
86164 TAATAATATTTTATTAAA
1 TAATAATAATTTATTAAA
86182 TAATAATAA
1 TAATAATAA
86191 CACCATCGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 1 0.04
21 12 0.48
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATAATTTATTAAA
Found at i:88284 original size:20 final size:20
Alignment explanation
Indices: 88247--88285 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
88237 AAACCATTCA
* *
88247 GGGGTGAATCGGTACCCTTT
1 GGGGGGAATCAGTACCCTTT
*
88267 GGGGGGAATCAGTTCCCTT
1 GGGGGGAATCAGTACCCTT
88286 GAGCAATCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.21, G:0.36, T:0.28
Consensus pattern (20 bp):
GGGGGGAATCAGTACCCTTT
Found at i:90874 original size:22 final size:22
Alignment explanation
Indices: 90843--90902 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
90833 TCGATTCCCT
*
90843 GGGGGAATCGGTTCCTCTTCAAA
1 GGGGGAATCGGTTCCCCTT-AAA
90866 GGGGG-ATCGGTTCCCCTTAAA
1 GGGGGAATCGGTTCCCCTTAAA
* *
90887 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
90903 TGCCTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 8 0.24
22 21 0.62
23 5 0.15
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTTAAA
Done.