Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009414.1 Hibiscus syriacus cultivar Beakdansim tig00113364_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: 104402
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:8069 original size:15 final size:15
Alignment explanation
Indices: 8037--8075 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
8027 AAAAAATCCG
*
8037 ACCCGATCGGGTCAGA
1 ACCC-ATCGGATCAGA
*
8053 ACCCATCGGATCGGA
1 ACCCATCGGATCAGA
8068 ACCCATCG
1 ACCCATCG
8076 AATTCGGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.26, C:0.36, G:0.26, T:0.13
Consensus pattern (15 bp):
ACCCATCGGATCAGA
Found at i:15087 original size:15 final size:15
Alignment explanation
Indices: 15067--15096 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15057 GTCGAAACCT
15067 TTGATTTTCAGAGAA
1 TTGATTTTCAGAGAA
15082 TTGATTTTCAGAGAA
1 TTGATTTTCAGAGAA
15097 ACATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (15 bp):
TTGATTTTCAGAGAA
Found at i:18613 original size:7 final size:7
Alignment explanation
Indices: 18597--18634 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
18587 GTCAAAGAAA
*
18597 GTCAATG
1 GTCAACG
18604 GTCAACG
1 GTCAACG
18611 GTCAACG
1 GTCAACG
18618 GTCAACG
1 GTCAACG
18625 GTCAACG
1 GTCAACG
18632 GTC
1 GTC
18635 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:18641 original size:5 final size:5
Alignment explanation
Indices: 18631--18688 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
18621 AACGGTCAAC
* *
18631 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
18680 GGTCG GGTC
1 GGTCG GGTC
18689 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:18652 original size:22 final size:22
Alignment explanation
Indices: 18624--18688 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
18614 AACGGTCAAC
18624 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
18646 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
18668 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
18689 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:18709 original size:19 final size:19
Alignment explanation
Indices: 18687--18782 Score: 90
Period size: 19 Copynumber: 5.1 Consensus size: 19
18677 TCGGGTCGGG
*
18687 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
18706 TCAGACCGGTC-AACCGGT
1 TCAGACCGGTCAAACCGGT
*
18724 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
18743 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
18763 TGAAACCGGTTAAACCGGT
1 TCAGACCGGTCAAACCGGT
18782 T
1 T
18783 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
17 1 0.02
18 15 0.23
19 33 0.51
20 16 0.25
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:18730 original size:10 final size:9
Alignment explanation
Indices: 18717--18782 Score: 60
Period size: 10 Copynumber: 6.9 Consensus size: 9
18707 CAGACCGGTC
18717 AACCGGTTCG
1 AACCGGTT-G
18727 AACCGGTTG
1 AACCGGTTG
**
18736 AAACCGGTCA
1 -AACCGGTTG
*
18746 AACCGGTCAG
1 AACCGGT-TG
18756 AACCGGTTG
1 AACCGGTTG
*
18765 AAACCGGTTA
1 -AACCGGTTG
18775 AACCGGTT
1 AACCGGTT
18783 TCCAGCAGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
9 17 0.36
10 30 0.64
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (9 bp):
AACCGGTTG
Found at i:18759 original size:29 final size:27
Alignment explanation
Indices: 18710--18782 Score: 53
Period size: 29 Copynumber: 2.6 Consensus size: 27
18700 ACCGATTCAG
18710 ACCGGTC-AACCGGTTCG-AACCGGTTGAA
1 ACCGGTCAAACCGGTT-GAAACCGG-T-AA
*
18738 ACCGGTCAAACCGG-TCAGAACCGGTTGAA
1 ACCGGTCAAACCGGTTGA-AACCGG-T-AA
*
18767 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
18783 TCCAGCAGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.21
29 30 0.77
30 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (27 bp):
ACCGGTCAAACCGGTTGAAACCGGTAA
Found at i:25938 original size:7 final size:7
Alignment explanation
Indices: 25922--25952 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
25912 GTCAAAGAAA
*
25922 GTCAATG
1 GTCAACG
25929 GTCAACG
1 GTCAACG
25936 GTCAACG
1 GTCAACG
25943 GTCAACG
1 GTCAACG
25950 GTC
1 GTC
25953 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:25968 original size:22 final size:22
Alignment explanation
Indices: 25942--25984 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
25932 AACGGTCAAC
25942 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
25964 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
25985 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:26028 original size:19 final size:19
Alignment explanation
Indices: 25987--26050 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
25977 GTCGGGTCAG
*
25987 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
26005 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
*
26025 ACCGGTTGAAACCGG-TCAGA
1 ACCGG-TCAAACCGGTTC-GA
26045 ACCGGT
1 ACCGGT
26051 TGAAAACCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:26038 original size:20 final size:21
Alignment explanation
Indices: 26013--26071 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
26003 CAGACCGGTC
26013 AAACCGGTTCGAACCGGTTG-
1 AAACCGGTTCGAACCGGTTGA
26033 AAACCGG-TCAGAACCGGTTGA
1 AAACCGGTTC-GAACCGGTTGA
*
26054 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCGAACCGGTT
26072 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 2 0.06
20 25 0.71
21 7 0.20
22 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCGAACCGGTTGA
Found at i:43147 original size:2 final size:2
Alignment explanation
Indices: 43142--43168 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43132 AAAATATTTT
43142 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
43169 TCACAATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45954 original size:14 final size:14
Alignment explanation
Indices: 45905--45957 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
45895 TTTTTCATTG
45905 AAAAACCGAACCGA
1 AAAAACCGAACCGA
* *
45919 AAAACCCGAACTGTTAA
1 AAAAACCGAACCG---A
45936 AAAAACCGAACCGA
1 AAAAACCGAACCGA
45950 AAAAACCG
1 AAAAACCG
45958 GTTTCAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
14 20 0.62
17 12 0.38
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.06
Consensus pattern (14 bp):
AAAAACCGAACCGA
Found at i:47997 original size:29 final size:28
Alignment explanation
Indices: 47939--48022 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
47929 AATATTCCCA
* **
47939 TCATGTTTTGTATGGGATCATATCAATG
1 TCATGTTTTGCATGGGATCATATCTCTG
47967 TCATGTTTCTGCATGGGATCATATCTCTG
1 TCATGTTT-TGCATGGGATCATATCTCTG
* * * *
47996 TCCTATTTATGCATGAGATCAAATCTC
1 TCATGTTT-TGCATGGGATCATATCTC
48023 AATCCTATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 8 0.17
29 39 0.83
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (28 bp):
TCATGTTTTGCATGGGATCATATCTCTG
Found at i:48028 original size:29 final size:29
Alignment explanation
Indices: 47976--48032 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
47966 GTCATGTTTC
* * **
47976 TGCATGGGATCATATCTCTGTCCTATTTA
1 TGCATGAGATCAAATCTCAATCCTATTTA
48005 TGCATGAGATCAAATCTCAATCCTATTT
1 TGCATGAGATCAAATCTCAATCCTATTT
48033 CTGTCTAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (29 bp):
TGCATGAGATCAAATCTCAATCCTATTTA
Found at i:53135 original size:147 final size:148
Alignment explanation
Indices: 52868--53180 Score: 486
Period size: 147 Copynumber: 2.1 Consensus size: 148
52858 TATAATTGCA
*
52868 CCGAAGTG-CCACATAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATCA
1 CCGAAG-GACCACGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATCA
* * *
52932 TTCCTTAAGAATCATATACATATAATAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATAACAAGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
52997 CCACAGAAT-ATATATATC
130 CCAAAGAATAATATATATC
* * *
53015 CCGAAGGATCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCAT
1 CCGAAGGACCACGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATCAT
** * *
53080 TCCTTAAGAATCATATACATATGCCAAGGATCACGTATGTGTCTCACCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATAACAAGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
53145 CAAAGAATACATATATATC
131 CAAAGAATA-ATATATATC
53164 CCGAAGGACCACGTAGA
1 CCGAAGGACCACGTAGA
53181 CCCTCGACTC
Statistics
Matches: 149, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
146 1 0.01
147 124 0.83
149 24 0.16
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (148 bp):
CCGAAGGACCACGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATCAT
TCCTTAAGAATCATATACATATAACAAGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATAATATATATC
Found at i:54503 original size:21 final size:21
Alignment explanation
Indices: 54479--54521 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
54469 TTTTGTTCGT
* * *
54479 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
54500 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
54521 T
1 T
54522 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:66576 original size:24 final size:24
Alignment explanation
Indices: 66549--66607 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
66539 AAGGAAATGA
*
66549 TTGTGGGGCTGGAAAAACAGCACC
1 TTGTGGGGCTGGAAAAACAGAACC
66573 TTGTGGGGCTGGAAAAACAGAACC
1 TTGTGGGGCTGGAAAAACAGAACC
66597 TTGTGGGGCTG
1 TTGTGGGGCTG
66608 TTATAAAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.17, G:0.37, T:0.20
Consensus pattern (24 bp):
TTGTGGGGCTGGAAAAACAGAACC
Found at i:73032 original size:16 final size:17
Alignment explanation
Indices: 73003--73034 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
72993 CGATCCGAAT
73003 TTTCGGATATCCAAAAA
1 TTTCGGATATCCAAAAA
73020 TTTCGGATA-CCAAAA
1 TTTCGGATATCCAAAA
73035 GTAATGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (17 bp):
TTTCGGATATCCAAAAA
Found at i:74117 original size:14 final size:14
Alignment explanation
Indices: 74084--74122 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
74074 ATCCGAATTT
* *
74084 TCGGATCAGATCAA
1 TCGGATCGGATTAA
74098 -CGGATCGGATTAA
1 TCGGATCGGATTAA
74111 TCGGATCGGATT
1 TCGGATCGGATT
74123 TTTTTGCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (14 bp):
TCGGATCGGATTAA
Found at i:76560 original size:218 final size:218
Alignment explanation
Indices: 76177--76619 Score: 879
Period size: 218 Copynumber: 2.0 Consensus size: 218
76167 AATGCTTAAT
76177 ACAAA-AATAAGTACTTAAACTATATCTAAAATTTACTTTTGACGTCTAATTTTGTTTTTGTTAA
1 ACAAAGAATAAGTACTTAAACTATATCTAAAATTTACTTTTGACGTCTAATTTTGTTTTTGTTAA
76241 AAATAAGCATTTAATATTTTTTTATATAATTAAAGTTTATATGATTATAGGATATAGAAAGATTT
66 AAATAAGCATTTAATATTTTTTTATATAATTAAAGTTTATATGATTATAGGATATAGAAAGATTT
76306 ATACAAATAATTAGAGATCCAATTTAATGTGTTAGGATAAAGGGATAAGAGATGTTAGATCATGC
131 ATACAAATAATTAGAGATCCAATTTAATGTGTTAGGATAAAGGGATAAGAGATGTTAGATCATGC
76371 ATGAGATCATGTACAAAGATGGG
196 ATGAGATCATGTACAAAGATGGG
76394 ACAAAGAATAAGTACTTAAACTATATCTAAAATTTACTTTTGACGTCTAATTTTGTTTTTGTTAA
1 ACAAAGAATAAGTACTTAAACTATATCTAAAATTTACTTTTGACGTCTAATTTTGTTTTTGTTAA
76459 AAATAAGCATTTAATATTTTTTTATATAATTAAAGTTTATATGATTATAGGATATAGAAAGATTT
66 AAATAAGCATTTAATATTTTTTTATATAATTAAAGTTTATATGATTATAGGATATAGAAAGATTT
76524 ATACAAATAATTAGAGATCCAATTTAATGTGTTAGGATAAAGGGATAAGAGATGTTAGATCATGC
131 ATACAAATAATTAGAGATCCAATTTAATGTGTTAGGATAAAGGGATAAGAGATGTTAGATCATGC
76589 ATGAGATCATGTACAAAGATGGG
196 ATGAGATCATGTACAAAGATGGG
76612 ACAAAGAA
1 ACAAAGAA
76620 CCCAGTTGAG
Statistics
Matches: 225, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
217 5 0.02
218 220 0.98
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (218 bp):
ACAAAGAATAAGTACTTAAACTATATCTAAAATTTACTTTTGACGTCTAATTTTGTTTTTGTTAA
AAATAAGCATTTAATATTTTTTTATATAATTAAAGTTTATATGATTATAGGATATAGAAAGATTT
ATACAAATAATTAGAGATCCAATTTAATGTGTTAGGATAAAGGGATAAGAGATGTTAGATCATGC
ATGAGATCATGTACAAAGATGGG
Found at i:92800 original size:20 final size:20
Alignment explanation
Indices: 92772--92816 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
92762 TTCTTTTAAT
* *
92772 ATTTTATTTTAAAAATAAAA
1 ATTTAATTTCAAAAATAAAA
* *
92792 ATTTAATTTCATAGATAAAA
1 ATTTAATTTCAAAAATAAAA
92812 ATTTA
1 ATTTA
92817 TTAAAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTAATTTCAAAAATAAAA
Found at i:93351 original size:20 final size:20
Alignment explanation
Indices: 93328--93366 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
93318 GTGTTCTCTC
93328 ATCTTCGTATGAGTTCTATT
1 ATCTTCGTATGAGTTCTATT
93348 ATCTTCGTATGAGTTCTAT
1 ATCTTCGTATGAGTTCTAT
93367 CATCATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (20 bp):
ATCTTCGTATGAGTTCTATT
Found at i:95041 original size:47 final size:48
Alignment explanation
Indices: 94916--95043 Score: 186
Period size: 48 Copynumber: 2.7 Consensus size: 48
94906 AACTGGTGCC
* * * *
94916 ACTCGGGCTAGTCAAGCTACTCAGTCAGAGGGACCGGAGAACGATTCG
1 ACTCCGGCTAGTCAATCTACTCAGTCAGAAGGACCGAAGAACGATTCG
* *
94964 ACTCCGGCTAGTCTATCTACTCTGTCAGAAGGACCGAAGAACGATTCG
1 ACTCCGGCTAGTCAATCTACTCAGTCAGAAGGACCGAAGAACGATTCG
*
95012 ACTCTGG-TAGTCAATCTACTCAGTCAGAAGGA
1 ACTCCGGCTAGTCAATCTACTCAGTCAGAAGGA
95044 TCAACTTTCT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 23 0.32
48 48 0.68
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (48 bp):
ACTCCGGCTAGTCAATCTACTCAGTCAGAAGGACCGAAGAACGATTCG
Found at i:95930 original size:14 final size:13
Alignment explanation
Indices: 95921--95960 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
95911 ACATATTAAA
95921 TAATAAATATAAT
1 TAATAAATATAAT
*
95934 TATATAACTATAAT
1 TA-ATAAATATAAT
95948 TAATAAATA-AAT
1 TAATAAATATAAT
95960 T
1 T
95961 TTAGGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 12 0.50
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAAATATAAT
Found at i:100184 original size:12 final size:12
Alignment explanation
Indices: 100164--100233 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
100154 GATACATGAC
*
100164 CTGAATTCTGTT
1 CTGATTTCTGTT
*
100176 CTGATTTCTGAT
1 CTGATTTCTGTT
*
100188 ATGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
100200 CAGATATCTGTT
1 CTGATTTCTGTT
*
100212 CTGAATTCTGTT
1 CTGATTTCTGTT
*
100224 TTGATTTCTG
1 CTGATTTCTG
100234 ATATCTACGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:100195 original size:24 final size:24
Alignment explanation
Indices: 100165--100237 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
100155 ATACATGACC
100165 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * * * *
100189 TGGATTCTGTTCAGATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATA
*
100213 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
100237 T
1 T
100238 CTACGTTTAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Done.