Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004196.1 Hibiscus syriacus cultivar Beakdansim tig00009175_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: 79932
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1538 original size:19 final size:19
Alignment explanation
Indices: 1514--1567 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1504 AGAATGTTTA
*
1514 AAAGTATCGATACTTATAT
1 AAAGTATCGATACTTATAC
* * *
1533 AAAGTATCGAAACTTTTGC
1 AAAGTATCGATACTTATAC
1552 AATAGTATCGATACTT
1 AA-AGTATCGATACTT
1568 TTGGGCTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (19 bp):
AAAGTATCGATACTTATAC
Found at i:12973 original size:17 final size:17
Alignment explanation
Indices: 12951--13022 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
12941 AATTAAGAGT
12951 TAGTTT-ATTAAATGAAC
1 TAGTTTAATT-AATGAAC
* *
12968 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
*
12985 TACTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
13002 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
13020 TAG
1 TAG
13023 ATGCATGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
17 32 0.68
18 15 0.32
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:13009 original size:18 final size:18
Alignment explanation
Indices: 12978--13021 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
12968 TAGTTTGATG
12978 AATGAACT-ACTTTAATT-
1 AATGAACTAACTTT-ATTC
12995 AATGAACTAACTTTATTC
1 AATGAACTAACTTTATTC
13013 AATGAACTA
1 AATGAACTA
13022 GATGCATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTATTC
Found at i:20819 original size:21 final size:23
Alignment explanation
Indices: 20777--20819 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
20767 AATTAAGTGA
*
20777 GAAGGAGAACGAGAGATGAAAGAC
1 GAAGGAGAACGAGACA-GAAAGAC
20801 GAAGGAGAA-GAGACA-AAAG
1 GAAGGAGAACGAGACAGAAAG
20820 GGTGAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
23 5 0.28
24 9 0.50
ACGTcount: A:0.53, C:0.07, G:0.37, T:0.02
Consensus pattern (23 bp):
GAAGGAGAACGAGACAGAAAGAC
Found at i:23413 original size:15 final size:15
Alignment explanation
Indices: 23393--23423 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
23383 AAGCAAGTAT
23393 GTGTAAACATGTTGC
1 GTGTAAACATGTTGC
23408 GTGTAAACATGTTGC
1 GTGTAAACATGTTGC
23423 G
1 G
23424 AGACTAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (15 bp):
GTGTAAACATGTTGC
Found at i:31725 original size:12 final size:12
Alignment explanation
Indices: 31708--31739 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
31698 CAATCCAGGC
31708 GACATACGGGGT
1 GACATACGGGGT
31720 GACATACGGGGT
1 GACATACGGGGT
31732 GACATACG
1 GACATACG
31740 ACCCATACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.38, T:0.16
Consensus pattern (12 bp):
GACATACGGGGT
Found at i:31848 original size:29 final size:29
Alignment explanation
Indices: 31795--31903 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
31785 AGGAATAGAG
* *
31795 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
*
31824 AGGTCGCCATGTAGTCCCGGTGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
31853 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
31882 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
31904 CCATTCCCAT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 73 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.30, G:0.32, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:32119 original size:25 final size:25
Alignment explanation
Indices: 32090--32141 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
32080 TGTACAATTA
32090 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
*
32115 TTGGTGAAATAATTGAGGCAGTCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
32140 TT
1 TT
32142 ATAAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.35, T:0.29
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGCCGG
Found at i:32182 original size:23 final size:23
Alignment explanation
Indices: 32154--32199 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
32144 AAAAGAAAGA
32154 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
**
32177 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
32200 CCGAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.35, T:0.13
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:32214 original size:25 final size:23
Alignment explanation
Indices: 32154--32214 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
32144 AAAAGAAAGA
**
32154 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
32177 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
32200 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
32215 AGGGAGAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 21 0.68
25 10 0.32
ACGTcount: A:0.51, C:0.07, G:0.33, T:0.10
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:32228 original size:21 final size:21
Alignment explanation
Indices: 32204--32256 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
32194 TTGCAGCCGA
32204 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
32225 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
32246 GAAAGTAAGAA
1 GAAAGAAAGAA
32257 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:32250 original size:17 final size:16
Alignment explanation
Indices: 32202--32233 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
32192 GATTGCAGCC
32202 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
32218 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
32234 AAAGGGAGAA
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:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:32522 original size:45 final size:45
Alignment explanation
Indices: 32419--32550 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
32409 TACATAAATT
*
32419 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTAGTTATA-TAA
*
32461 AAAAA-TAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
*
32505 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAT
32551 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 19 0.25
46 5 0.07
47 7 0.09
48 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
Found at i:32744 original size:16 final size:16
Alignment explanation
Indices: 32712--32758 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
32702 TTTAAAAAGT
*
32712 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
32728 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
32744 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
32759 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:32753 original size:15 final size:14
Alignment explanation
Indices: 32733--32763 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
32723 GTTTATTAGT
32733 TTATTATATTATAAG
1 TTATTATATTA-AAG
32748 TTATTATATTAAAG
1 TTATTATATTAAAG
32762 TT
1 TT
32764 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:34927 original size:26 final size:25
Alignment explanation
Indices: 34893--35232 Score: 294
Period size: 26 Copynumber: 13.6 Consensus size: 25
34883 TATTTAAATC
*
34893 ATTATTAAATCATTTTTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
34919 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
34945 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * *
34971 ATTATCAAATCATTACTA-AATCATCAA
1 ATTAT-AAATCATTATTATAATGAT--T
* *
34998 ATCATTAAAT-A-T-TTA-AATCATT
1 ATTA-TAAATCATTATTATAATGATT
*
35020 A-T-TAAATCATTTTTATAATGATT
1 ATTATAAATCATTATTATAATGATT
35043 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
35069 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
* * * *
35095 ATTATCAAATCATTACTAATCATCA-A
1 ATTAT-AAATCATTA-TTATAATGATT
* *
35121 ATCATTAAAT-A-T-TTA-AATCATT
1 ATTA-TAAATCATTATTATAATGATT
*
35143 A-T-TAAATCATTTTTATAATGATT
1 ATTATAAATCATTATTATAATGATT
35166 ATTACTAAATCATTATTATAATGATT
1 ATTA-TAAATCATTATTATAATGATT
*
35192 ATTATCAAATCATTACTATAATGATT
1 ATTAT-AAATCATTATTATAATGATT
35218 ATTATCAAATCATTA
1 ATTAT-AAATCATTA
35233 CTAAATCATC
Statistics
Matches: 266, Mismatches: 25, Indels: 46
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.04
20 2 0.01
21 6 0.02
22 10 0.04
23 14 0.05
24 11 0.04
25 10 0.04
26 189 0.71
27 13 0.05
28 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (25 bp):
ATTATAAATCATTATTATAATGATT
Found at i:35069 original size:23 final size:23
Alignment explanation
Indices: 34893--35296 Score: 149
Period size: 26 Copynumber: 16.4 Consensus size: 23
34883 TATTTAAATC
* *
34893 ATTATTAAATCATTTTTATAATG
1 ATTAATAAATCATTATTATAATG
34916 ATTATTACTAAATCATTATTATAATG
1 ATTA--A-TAAATCATTATTATAATG
*
34942 ATTATTATCAAATCATTACTATAATG
1 ATTA--AT-AAATCATTATTATAATG
* *
34968 ATTATTATCAAATCATTACTA-AATC
1 ATTA--AT-AAATCATTATTATAATG
* * * * * *
34993 ATCAAATCATTAAATATT-TAAATC
1 AT-TAATAAATCATTATTAT-AATG
* *
35017 ATTATTAAATCATTTTTATAATG
1 ATTAATAAATCATTATTATAATG
35040 ATTATTACTAAATCATTATTATAATG
1 ATTA--A-TAAATCATTATTATAATG
*
35066 ATTATTATCAAATCATTACTATAATG
1 ATTA--AT-AAATCATTATTATAATG
* * *
35092 ATTATTATCAAATCATTACTAATCATCAA
1 ATTA--AT-AAATCATTA-TTATAAT--G
* * *
35121 ATCATTAAAT-A-T-TTA-AATC
1 ATTAATAAATCATTATTATAATG
* *
35140 ATTATTAAATCATTTTTATAATG
1 ATTAATAAATCATTATTATAATG
35163 ATTATTACTAAATCATTATTATAATG
1 ATTA--A-TAAATCATTATTATAATG
*
35189 ATTATTATCAAATCATTACTATAATG
1 ATTA--AT-AAATCATTATTATAATG
* *
35215 ATTATTATCAAATCATTACTA-AATC
1 ATTA--AT-AAATCATTATTATAATG
* * * * * *
35240 ATCAAATCATTAAATATT-TAAATC
1 AT-TAATAAATCATTATTAT-AATG
* *
35264 ATTATTAAATCATTTTTATAATG
1 ATTAATAAATCATTATTATAATG
35287 ATTAATAAAT
1 ATTAATAAAT
35297 ACATAGAAAT
Statistics
Matches: 303, Mismatches: 51, Indels: 54
0.74 0.12 0.13
Matches are distributed among these distances:
19 9 0.03
20 1 0.00
21 3 0.01
22 5 0.02
23 58 0.19
24 19 0.06
25 14 0.05
26 186 0.61
27 5 0.02
29 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTAATAAATCATTATTATAATG
Found at i:35078 original size:124 final size:124
Alignment explanation
Indices: 34858--35290 Score: 859
Period size: 124 Copynumber: 3.5 Consensus size: 124
34848 TTTTCTATTT
34858 ATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTA
1 ATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTA
34923 CTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATC
66 CTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATC
34982 ATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTA
1 ATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTA
35047 CTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATC
66 CTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATC
35106 ATTACT-AATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTA
1 ATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTA
35170 CTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATC
66 CTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATC
35229 ATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTA
1 ATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTA
35291 ATAAATACAT
Statistics
Matches: 308, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
123 123 0.40
124 185 0.60
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (124 bp):
ATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTA
CTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATC
Found at i:35116 original size:15 final size:14
Alignment explanation
Indices: 34925--35235 Score: 76
Period size: 12 Copynumber: 22.9 Consensus size: 14
34915 GATTATTACT
*
34925 AAATCATTATTAT-
1 AAATCATTACTATC
* *
34938 -AATGATTATTATC
1 AAATCATTACTATC
34951 AAATCATTACTAT-
1 AAATCATTACTATC
* *
34964 -AATGATTATTATC
1 AAATCATTACTATC
34977 AAATCATTACTAAATCATC
1 AAATCATTAC----T-ATC
* *
34996 AAATCATTAAATATTT
1 AAATCATT-ACTA-TC
35012 AAATCATTA-T-T-
1 AAATCATTACTATC
**
35023 AAATCATTTTTAT-
1 AAATCATTACTATC
* *
35036 -AATGATTATTA-C
1 AAATCATTACTATC
*
35048 TAAATCATTATTAT-
1 -AAATCATTACTATC
* *
35062 -AATGATTATTATC
1 AAATCATTACTATC
35075 AAATCATTACTAT-
1 AAATCATTACTATC
* *
35088 -AATGATTATTATC
1 AAATCATTACTATC
35101 AAATCATTACTAATCATC
1 AAATCATTAC---T-ATC
* *
35119 AAATCATTAAATATTT
1 AAATCATT-ACTA-TC
35135 AAATCATTA-T-T-
1 AAATCATTACTATC
**
35146 AAATCATTTTTAT-
1 AAATCATTACTATC
* *
35159 -AATGATTATTA-C
1 AAATCATTACTATC
*
35171 TAAATCATTATTAT-
1 -AAATCATTACTATC
* *
35185 -AATGATTATTATC
1 AAATCATTACTATC
35198 AAATCATTACTAT-
1 AAATCATTACTATC
* *
35211 -AATGATTATTATC
1 AAATCATTACTATC
35224 AAATCATTACTA
1 AAATCATTACTA
35236 AATCATCAAA
Statistics
Matches: 228, Mismatches: 33, Indels: 73
0.68 0.10 0.22
Matches are distributed among these distances:
11 16 0.07
12 85 0.37
13 2 0.01
14 75 0.33
15 4 0.02
16 20 0.09
17 1 0.00
18 12 0.05
19 12 0.05
20 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:38175 original size:26 final size:24
Alignment explanation
Indices: 38117--38175 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
38107 CTAATAAACC
*
38117 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
38141 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
38169 TAATAAT
1 TAATAAT
38176 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:39024 original size:28 final size:30
Alignment explanation
Indices: 38984--39046 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
38974 ATTTTTTATA
*
38984 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
39014 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
39042 TAATA
1 TAATA
39047 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:39053 original size:28 final size:28
Alignment explanation
Indices: 38988--39053 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
38978 TTTATATAAT
*
38988 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
39016 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
39044 ATAATTTATA
1 ATAATATATA
39054 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:39056 original size:21 final size:21
Alignment explanation
Indices: 39023--39071 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
39013 CTAATATAAT
39023 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
39044 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
39065 ATTAACT
1 A-TAACT
39072 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:39548 original size:16 final size:16
Alignment explanation
Indices: 39527--39580 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
39517 CAATGCACAG
39527 CATGCATCCCCTCCCC
1 CATGCATCCCCTCCCC
* *
39543 CATGCATTCCC-ACCC
1 CATGCATCCCCTCCCC
39558 CATGCATCCCCTCCCC
1 CATGCATCCCCTCCCC
39574 CATGCAT
1 CATGCAT
39581 TCCCACGTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 13 0.39
16 20 0.61
ACGTcount: A:0.17, C:0.56, G:0.07, T:0.20
Consensus pattern (16 bp):
CATGCATCCCCTCCCC
Found at i:39560 original size:15 final size:15
Alignment explanation
Indices: 39540--39586 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
39530 GCATCCCCTC
39540 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
39555 CCCCATGCATCCCCTC
1 CCCCATGCATTCCC-A
39571 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
39586 C
1 C
39587 GTCCCATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.17, C:0.57, G:0.06, T:0.19
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:39562 original size:31 final size:31
Alignment explanation
Indices: 39527--39586 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
39517 CAATGCACAG
39527 CATGCATCCCCTCCCCCATGCATTCCCACCC
1 CATGCATCCCCTCCCCCATGCATTCCCACCC
39558 CATGCATCCCCTCCCCCATGCATTCCCAC
1 CATGCATCCCCTCCCCCATGCATTCCCAC
39587 GTCCCATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.17, C:0.57, G:0.07, T:0.20
Consensus pattern (31 bp):
CATGCATCCCCTCCCCCATGCATTCCCACCC
Found at i:39675 original size:29 final size:29
Alignment explanation
Indices: 39633--39722 Score: 137
Period size: 29 Copynumber: 3.1 Consensus size: 29
39623 AAATACACAC
39633 AGGTCGCCCGGATGCCATGGCGACCTCTA
1 AGGTCGCCCGGATGCCATGGCGACCTCTA
*
39662 AGGTCGCCCGGATGCCATGGCGACCT-TGG
1 AGGTCGCCCGGATGCCATGGCGACCTCT-A
* *
39691 AGGTCGCCCGGATGCCATGGAGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCTA
39720 AGG
1 AGG
39723 CCACTGTAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
28 1 0.02
29 54 0.98
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCTA
Found at i:58891 original size:21 final size:21
Alignment explanation
Indices: 58861--58907 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
58851 CAAGGTAAGA
*
58861 GTATCGATACTCCCTATAGGG
1 GTATCAATACTCCCTATAGGG
58882 GTATCAATACTCCCTATAGGG
1 GTATCAATACTCCCTATAGGG
58903 GTATC
1 GTATC
58908 GATATTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (21 bp):
GTATCAATACTCCCTATAGGG
Found at i:78863 original size:42 final size:43
Alignment explanation
Indices: 78766--78930 Score: 160
Period size: 41 Copynumber: 3.8 Consensus size: 43
78756 AAATGATTTC
* *
78766 ATTGAAGGCCCCTACATTTTTTTTGAATCTCACATTTTACATT-TA
1 ATTGAAGGCCCCTA-A--TTTTTTCAATCTCACTTTTTACATTATA
* *
78811 ACT-AAGGCCCCTAATTTTTTCAATCTAACTTTTTACATTATA
1 ATTGAAGGCCCCTAATTTTTTCAATCTCACTTTTTACATTATA
*
78853 ATTGAA-GCCCCT-ATTTTTTCAATCCCACTTTTTACATTTATA
1 ATTGAAGGCCCCTAATTTTTTCAATCTCACTTTTTACA-TTATA
* ** * *
78895 ATTG-AGACTACTAATTTTTTTTATTCTCACTTTTTA
1 ATTGAAGGCCCCTAA-TTTTTTCAATCTCACTTTTTA
78931 TCTTTAATTG
Statistics
Matches: 101, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
41 45 0.45
42 22 0.22
43 4 0.04
44 28 0.28
45 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (43 bp):
ATTGAAGGCCCCTAATTTTTTCAATCTCACTTTTTACATTATA
Done.