Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008390.1 Hibiscus syriacus cultivar Beakdansim tig00111155_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: 61190
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1663 original size:19 final size:20
Alignment explanation
Indices: 1641--1684 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1631 GAGAAAAGGT
1641 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
1660 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
1680 AAAAG
1 AAAAG
1685 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:8054 original size:17 final size:16
Alignment explanation
Indices: 8032--8065 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
8022 TAAAAACAGT
8032 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
8049 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
8065 A
1 A
8066 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:8586 original size:24 final size:24
Alignment explanation
Indices: 8542--8588 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
8532 ATAAAGAACC
*
8542 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
8566 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
8589 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:12218 original size:13 final size:13
Alignment explanation
Indices: 12200--12225 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12190 GGAAGTCAAC
12200 GGTCAACGGGTCG
1 GGTCAACGGGTCG
12213 GGTCAACGGGTCG
1 GGTCAACGGGTCG
12226 AGTCGGGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:22192 original size:18 final size:19
Alignment explanation
Indices: 22169--22211 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
22159 CAGTAATCCT
22169 ATTCC-CTGATAATCTTAC
1 ATTCCACTGATAATCTTAC
* *
22187 ATTCCCACTGATAATTTTAT
1 ATT-CCACTGATAATCTTAC
22207 ATTCC
1 ATTCC
22212 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.28, C:0.26, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:22199 original size:20 final size:20
Alignment explanation
Indices: 22174--22211 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22164 ATCCTATTCC
22174 CTGATAATCTTACATTCCCA
1 CTGATAATCTTACATTCCCA
* *
22194 CTGATAATTTTATATTCC
1 CTGATAATCTTACATTCC
22212 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:24152 original size:3 final size:3
Alignment explanation
Indices: 24144--24176 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
24134 AAGCATTGGG
*
24144 ATA ATA ATA AAA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24177 TTGTTTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:27547 original size:15 final size:15
Alignment explanation
Indices: 27527--27555 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27517 TTTGCTTTGT
27527 TAAATTAAAATAAAA
1 TAAATTAAAATAAAA
27542 TAAATTAAAATAAA
1 TAAATTAAAATAAA
27556 GTTACTCTTC
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATTAAAATAAAA
Found at i:27933 original size:14 final size:15
Alignment explanation
Indices: 27894--27935 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
27884 AAACTAAAGT
*
27894 AAATAAATCAA-TGA
1 AAATAAATAAAGTGA
*
27908 AACTAAATAAAGTGA
1 AAATAAATAAAGTGA
27923 AAATAAA-AAAGTG
1 AAATAAATAAAGTG
27936 TAACACCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.19
Consensus pattern (15 bp):
AAATAAATAAAGTGA
Found at i:32170 original size:26 final size:22
Alignment explanation
Indices: 32118--32169 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
32108 GCGATGCTAA
*
32118 CCACCCACTAGCGGCTCTAACC
1 CCACCCACTAACGGCTCTAACC
*
32140 CCACCCACTAACGGCTCTAACT
1 CCACCCACTAACGGCTCTAACC
32162 CCACCCAC
1 CCACCCAC
32170 CATTATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.52, G:0.10, T:0.13
Consensus pattern (22 bp):
CCACCCACTAACGGCTCTAACC
Found at i:38398 original size:21 final size:21
Alignment explanation
Indices: 38372--38411 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38362 CCCCATTTGA
*
38372 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
38393 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
38412 CTGGGGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:43522 original size:3 final size:3
Alignment explanation
Indices: 43516--43541 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43506 CCACCAATGG
43516 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
43542 ACAACAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:46998 original size:29 final size:29
Alignment explanation
Indices: 46964--47044 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
46954 TTATGGTTGC
*
46964 CATTTTAGGTTGTAACATATTTCCAACCA
1 CATTTTAGGTTGTAACACATTTCCAACCA
* * *
46993 TATTTTAGGTTGTAATACATTTCCAATCA
1 CATTTTAGGTTGTAACACATTTCCAACCA
* *
47022 CATTTTAGGTTGCATCACATTTC
1 CATTTTAGGTTGTAACACATTTC
47045 TAATATGCTC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (29 bp):
CATTTTAGGTTGTAACACATTTCCAACCA
Found at i:50711 original size:20 final size:19
Alignment explanation
Indices: 50688--50727 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
50678 TAGTCACCAA
*
50688 AATTAGGTTTTATATATTTT
1 AATTAGGTTTT-CATATTTT
*
50708 AATTTGGTTTTCATATTTT
1 AATTAGGTTTTCATATTTT
50727 A
1 A
50728 TTTACTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.60
Consensus pattern (19 bp):
AATTAGGTTTTCATATTTT
Found at i:53251 original size:18 final size:18
Alignment explanation
Indices: 53228--53269 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
53218 ATTACATCAT
53228 TTCATACATGCATTTACA
1 TTCATACATGCATTTACA
** *
53246 TTCATATTTGTATTTACA
1 TTCATACATGCATTTACA
53264 TTCATA
1 TTCATA
53270 TTTCACATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.48
Consensus pattern (18 bp):
TTCATACATGCATTTACA
Found at i:55430 original size:3 final size:3
Alignment explanation
Indices: 55422--55455 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
55412 GACATCACAT
55422 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55456 AATTTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55911 original size:42 final size:43
Alignment explanation
Indices: 55836--55931 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 43
55826 ATTTTAATTA
55836 AATAATAATAATAATAAAAATTGTCAACTCATATAGAAATAAT
1 AATAATAATAATAATAAAAATTGTCAACTCATATAGAAATAAT
*
55879 AATAATAATAATAAT-AAAATTGTCAAGTCATATAGAAATAAT
1 AATAATAATAATAATAAAAATTGTCAACTCATATAGAAATAAT
55921 AATAA-AATAAT
1 AATAATAATAAT
55932 TTAGAGGGGT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
41 6 0.12
42 31 0.60
43 15 0.29
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (43 bp):
AATAATAATAATAATAAAAATTGTCAACTCATATAGAAATAAT
Done.