Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008663.1 Hibiscus syriacus cultivar Beakdansim tig00111665_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: 91981
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2045 original size:105 final size:104
Alignment explanation
Indices: 1920--2116 Score: 340
Period size: 105 Copynumber: 1.9 Consensus size: 104
1910 GATGTAGCTC
*
1920 AACCTAGCCTCACTTCGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTTTCGATCTAGGAA
1 AACCTAGCCTCACTTCGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTTTCAATCTA-GAA
*
1985 AGCAACAAGGATCCTGCACAAATAAGAAATGATACAGTTA
65 AGCAACAAGGATCCTGCACAAACAAGAAATGATACAGTTA
* * *
2025 AACCTAGCCTCACTTGGATGGATGGTGAAGTTAAGGTTGTACCTTTGATTGTTTCAATCTAGAAA
1 AACCTAGCCTCACTTCGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTTTCAATCTAGAAA
2090 GCAACAAGGATCCTGCACAAACAAGAA
66 GCAACAAGGATCCTGCACAAACAAGAA
2117 GCTCAAAAAA
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
104 30 0.34
105 57 0.66
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (104 bp):
AACCTAGCCTCACTTCGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTTTCAATCTAGAAA
GCAACAAGGATCCTGCACAAACAAGAAATGATACAGTTA
Found at i:16190 original size:24 final size:21
Alignment explanation
Indices: 16155--16197 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
16145 GGCTCATTCT
*
16155 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
16178 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
16198 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:18028 original size:19 final size:20
Alignment explanation
Indices: 18004--18054 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
17994 CGGCCAAGAG
* *
18004 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
18023 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
18043 CATGTATTTTCA
1 CATGTATTTTCA
18055 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:22212 original size:19 final size:20
Alignment explanation
Indices: 22188--22238 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
22178 CGGCCAAGAG
* *
22188 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
22207 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
22227 CATGTATTTTCA
1 CATGTATTTTCA
22239 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:30402 original size:19 final size:18
Alignment explanation
Indices: 30362--30408 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
30352 TTTGAATTAT
*
30362 TTTTCTTTTCTTTTCTTC
1 TTTTCTTTTCTTTTCTTA
30380 TTTTCTTCTTCTTTT-TGTA
1 TTTTCTT-TTCTTTTCT-TA
30399 TTTTTCTTTT
1 -TTTTCTTTT
30409 TGCACTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCTTA
Found at i:30788 original size:20 final size:21
Alignment explanation
Indices: 30751--30789 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
30741 GATGGTCTTG
*
30751 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
30772 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
30790 GTGGTGCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:32616 original size:35 final size:36
Alignment explanation
Indices: 32577--32656 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 36
32567 AAATGGAATT
**
32577 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
32612 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
32648 TGGTGATGA
1 TGGTGATGA
32657 ACATATTGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 21 0.50
36 21 0.50
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
Found at i:38167 original size:36 final size:35
Alignment explanation
Indices: 38089--38173 Score: 125
Period size: 35 Copynumber: 2.4 Consensus size: 35
38079 AATGGAAATC
* *
38089 GAATTTGGTGATGATATAGGCGTGATGTGGTGATG
1 GAATATGGTGATGATATAGGCGTGATATGGTGATG
* *
38124 GACTATGGAGATGATATAGGCGTGATAATGGTGATG
1 GAATATGGTGATGATATAGGCGTGAT-ATGGTGATG
38160 GAATATGGTGATGA
1 GAATATGGTGATGA
38174 ACAGATTGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 23 0.53
36 20 0.47
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (35 bp):
GAATATGGTGATGATATAGGCGTGATATGGTGATG
Found at i:40643 original size:11 final size:11
Alignment explanation
Indices: 40570--40649 Score: 56
Period size: 11 Copynumber: 6.8 Consensus size: 11
40560 TACAATTTGT
*
40570 TCATCACCATCT
1 TCATCACCAT-A
40582 TCCATCACCATTA
1 T-CATCACCA-TA
*
40595 TCA-CGCCTATA
1 TCATCACC-ATA
*
40606 TCATTACCATA
1 TCATCACCATA
40617 GTCCATCACCATA
1 -T-CATCACCATA
40630 TCA-CACCTATA
1 TCATCACC-ATA
40641 TCATCACCA
1 TCATCACCA
40650 AATTCCATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
10 4 0.07
11 20 0.36
12 12 0.22
13 18 0.33
14 1 0.02
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:40657 original size:35 final size:36
Alignment explanation
Indices: 40570--40657 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
40560 TACAATTTGT
* *
40570 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACACCTATA
* *
40606 TCATTACCATAGTCCATCACCA-TATCACACCTATA
1 TCATCACCATATTCCATCACCATTATCACACCTATA
*
40641 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
40658 TTCCATTTCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 26 0.58
36 19 0.42
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACACCTATA
Found at i:47698 original size:19 final size:20
Alignment explanation
Indices: 47657--47707 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
47647 GAAACCCCTT
*
47657 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
47677 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
47696 TGAAGATACATG
1 TGAAAATACATG
47708 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:51125 original size:11 final size:10
Alignment explanation
Indices: 51074--51125 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
51064 TTTTGAATTC
*
51074 TTTTCTTTTC
1 TTTTCTTTTT
51084 TTTTCTTCTTT
1 TTTTCTT-TTT
*
51095 TCTTCTTCTTT
1 TTTTCTT-TTT
*
51106 TTGTCTTTTT
1 TTTTCTTTTT
*
51116 CTTTCTTTTT
1 TTTTCTTTTT
51126 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:51126 original size:18 final size:18
Alignment explanation
Indices: 51072--51126 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
51062 CTTTTTGAAT
51072 TCTTTTCTTTTCTTTTCT-
1 TCTTTTCTTTTCTTTT-TG
51090 TCTTTTCTTCTTCTTTTTG
1 TCTTTTCTT-TTCTTTTTG
51109 TCTTTT-TCTTTCTTTTTG
1 TCTTTTCT-TTTCTTTTTG
51127 CACTCCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 20 0.59
19 14 0.41
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (18 bp):
TCTTTTCTTTTCTTTTTG
Found at i:51889 original size:19 final size:20
Alignment explanation
Indices: 51848--51898 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
51838 GAAACCCCTT
*
51848 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
51868 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
51887 TGAAGATACATG
1 TGAAAATACATG
51899 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:75570 original size:28 final size:26
Alignment explanation
Indices: 75517--75573 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
75507 TTCTTTGCTT
* *
75517 TTTCTTCTTTTGAGTGCTGGATTTTC
1 TTTCTTCTTTTGAGTGCTGCAATTTC
*
75543 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTGCTGCAATTTC
75571 TTT
1 TTT
75574 TCCGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 7 0.27
28 15 0.58
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTTTGAGTGCTGCAATTTC
Found at i:77620 original size:14 final size:14
Alignment explanation
Indices: 77601--77637 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
77591 TAAGATACTA
77601 TTTCCATCACCATC
1 TTTCCATCACCATC
77615 TTTCCATCACCATC
1 TTTCCATCACCATC
*
77629 -CTCCATCAC
1 TTTCCATCAC
77638 TTTCACACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.32
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:80297 original size:32 final size:33
Alignment explanation
Indices: 80259--80325 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
80249 CAAAAATTAA
80259 AAGAAA-GAAATGATTAA-AATTGAATATGGA-AG
1 AAGAAAGGAAATGA-TAAGAATTGAA-ATGGATAG
80291 AAGAAAGGAAATGATAAGAATTGAAATGGATAG
1 AAGAAAGGAAATGATAAGAATTGAAATGGATAG
80324 AA
1 AA
80326 ATGTTAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (33 bp):
AAGAAAGGAAATGATAAGAATTGAAATGGATAG
Found at i:80889 original size:19 final size:20
Alignment explanation
Indices: 80848--80898 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
80838 GAAACCCCTT
*
80848 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
80868 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
80887 TGAATATACATG
1 TGAAAATACATG
80899 CTCTTGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:90280 original size:35 final size:35
Alignment explanation
Indices: 90241--90342 Score: 132
Period size: 35 Copynumber: 2.9 Consensus size: 35
90231 ATTGGTGGTT
*
90241 ATATAGGCGTGAAATGGTGATAGAAGATGGTAATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
* * * *
90276 ATATAGGCGTGCAATGGTAATGGAATATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
* *
90311 TTATAGGCCTGAAAATGGTGATGGAAGATGGT
1 ATATAGGCGTG-AAATGGTGATGGAAGATGGT
90343 GATGTTTAGG
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 39 0.70
36 17 0.30
ACGTcount: A:0.33, C:0.05, G:0.34, T:0.27
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
Done.