Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007181.1 Hibiscus syriacus cultivar Beakdansim tig00018863_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: 58875
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:5024 original size:13 final size:14
Alignment explanation
Indices: 5006--5038 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4996 TATGCCCTTC
*
5006 CCCTAACTTA-AAA
1 CCCTAAATTATAAA
5019 CCCTAAATTATAAA
1 CCCTAAATTATAAA
5033 CCCTAA
1 CCCTAA
5039 GTTTGTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAAATTATAAA
Found at i:9291 original size:28 final size:28
Alignment explanation
Indices: 9204--9356 Score: 155
Period size: 29 Copynumber: 5.4 Consensus size: 28
9194 CCAGTTACAT
* * * *
9204 TTTTGGGAATT-TTTTAAAAATAGTGACA
1 TTTTGGTAATTATTTTTAAAA-GGTGATA
* * * *
9232 TTCTGGTAATTATTTTTAAAACGATAACA
1 TTTTGGTAATTATTTTTAAAA-GGTGATA
* * *
9261 TTTTGGGAATTATTTGTAAACGGTGATA
1 TTTTGGTAATTATTTTTAAAAGGTGATA
*
9289 TTTTGGTAATTATTTTTAAAATAGTGATA
1 TTTTGGTAATTATTTTTAAAA-GGTGATA
9318 TTTTGGTAATTATTTTTAAAAGGTGATA
1 TTTTGGTAATTATTTTTAAAAGGTGATA
*
9346 TTTTTGTAATT
1 TTTTGGTAATT
9357 TTCAAATGTG
Statistics
Matches: 103, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
28 47 0.46
29 56 0.54
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (28 bp):
TTTTGGTAATTATTTTTAAAAGGTGATA
Found at i:9321 original size:57 final size:57
Alignment explanation
Indices: 9204--9356 Score: 168
Period size: 57 Copynumber: 2.7 Consensus size: 57
9194 CCAGTTACAT
* * * *
9204 TTTTGGGAATT-TTT-TAAAAATAGTGACATTCTGGTAATTATTTTTAAAACGATAACA
1 TTTTGGGAATTATTTGT-AAAA-GGTGATATTTTGGTAATTATTTTTAAAAAGATAACA
* * *
9261 TTTTGGGAATTATTTGTAAACGGTGATATTTTGGTAATTATTTTTAAAATAG-TGATA
1 TTTTGGGAATTATTTGTAAAAGGTGATATTTTGGTAATTATTTTTAAAA-AGATAACA
* * *
9318 TTTTGGTAATTATTTTTAAAAGGTGATATTTTTGTAATT
1 TTTTGGGAATTATTTGTAAAAGGTGATATTTTGGTAATT
9357 TTCAAATGTG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
57 74 0.90
58 7 0.09
59 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (57 bp):
TTTTGGGAATTATTTGTAAAAGGTGATATTTTGGTAATTATTTTTAAAAAGATAACA
Found at i:21735 original size:154 final size:154
Alignment explanation
Indices: 21450--21918 Score: 866
Period size: 154 Copynumber: 3.0 Consensus size: 154
21440 CCTGAAATTG
*
21450 ATCACCCCTTCCACTGCCAACACCATTTGACTCTTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
1 ATCATCCCTTCCACTGCCAACACCATTTGACTCTTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
21515 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
66 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
* *
21580 GCACTTGAACTGTGCTTTGCTTCA
131 GCACGTGAACTATGCTTTGCTTCA
*
21604 ATCATCCCTTCCACTGCCAACACCATTTGACTATTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
1 ATCATCCCTTCCACTGCCAACACCATTTGACTCTTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
21669 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
66 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
21734 GCACGTGAACTATGCTTTGCTTCA
131 GCACGTGAACTATGCTTTGCTTCA
*
21758 ATCATCCCTTCCACTGCCAACACCATTTGACTCCTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
1 ATCATCCCTTCCACTGCCAACACCATTTGACTCTTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
* * *
21823 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTATTTATCATTGTGCTTCTTGTGCATTTGATCT
66 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
21888 GCACGTGAACTATGCTTTGCTTCA
131 GCACGTGAACTATGCTTTGCTTCA
21912 ATCATCC
1 ATCATCC
21919 ATTGCTGCAA
Statistics
Matches: 306, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 306 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (154 bp):
ATCATCCCTTCCACTGCCAACACCATTTGACTCTTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
GCACGTGAACTATGCTTTGCTTCA
Found at i:26338 original size:19 final size:20
Alignment explanation
Indices: 26314--26366 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
26304 AAAATCTTGA
26314 GTGCATCGATGCATGGTAT-
1 GTGCATCGATGCATGGTATG
*
26333 GTGCATCGATGCATGGTTTG
1 GTGCATCGATGCATGGTATG
*
26353 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
26367 CACTTTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATGGTATG
Found at i:26726 original size:21 final size:22
Alignment explanation
Indices: 26702--26753 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
26692 TTTGAAATTA
*
26702 CTCCCCCTTAC-TTTGACACTT
1 CTCCCCCTTACATTTAACACTT
* * *
26723 CTCCCCATAACATTTAACATTT
1 CTCCCCCTTACATTTAACACTT
26745 CTCCCCCTT
1 CTCCCCCTT
26754 TTTGTTAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.19, C:0.42, G:0.02, T:0.37
Consensus pattern (22 bp):
CTCCCCCTTACATTTAACACTT
Found at i:28199 original size:19 final size:19
Alignment explanation
Indices: 28175--28226 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
28165 TTTAAGCAGG
28175 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
28194 TGCATCGATGCACTGCTTA
1 TGCATCGATGCACTCCTTA
28213 TGCATCGATGCACT
1 TGCATCGATGCACT
28227 AATTGCATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:31017 original size:30 final size:30
Alignment explanation
Indices: 30718--31000 Score: 539
Period size: 30 Copynumber: 9.4 Consensus size: 30
30708 TCCGAAGGAC
30718 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
30748 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
30778 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
30808 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
30838 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
30868 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
30898 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
30928 CTATCCAGATGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
30958 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
30988 CTATCCATAGGTC
1 CTATCCAGAGGTC
31001 CCGAAGAACC
Statistics
Matches: 248, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 248 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:31040 original size:31 final size:31
Alignment explanation
Indices: 30986--31078 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
30976 GATCCTCGGT
* *
30986 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
31017 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
31048 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
31079 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:35581 original size:30 final size:30
Alignment explanation
Indices: 35312--35564 Score: 488
Period size: 30 Copynumber: 8.4 Consensus size: 30
35302 TCCGAAGGAC
35312 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
35342 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
35372 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
35402 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
35432 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
35462 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
35492 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
35522 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
35552 CTATCCATAGGTC
1 CTATCCAGAGGTC
35565 CCGAAGAACC
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 220 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:35604 original size:31 final size:31
Alignment explanation
Indices: 35550--35642 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
35540 GATCCTCGGT
* *
35550 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
35581 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
35612 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
35643 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:35924 original size:13 final size:13
Alignment explanation
Indices: 35873--35925 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
35863 ATATTCTGTA
35873 TATTTCATATTCT
1 TATTTCATATTCT
*
35886 T-TCTT-ATA-TCC
1 TAT-TTCATATTCT
35897 T-TTTCATACTTCT
1 TATTTCATA-TTCT
35910 TATTTCATATTCT
1 TATTTCATATTCT
35923 TAT
1 TAT
35926 GAAATCATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
10 2 0.06
11 7 0.21
12 4 0.12
13 13 0.39
14 7 0.21
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTCATATTCT
Found at i:36005 original size:2 final size:2
Alignment explanation
Indices: 35993--36031 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
35983 TACACAACTC
35993 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36032 TGTAACATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37652 original size:20 final size:20
Alignment explanation
Indices: 37602--37653 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
37592 ACCCGATAGA
*
37602 TGCATCGATGCATGGCCTTG
1 TGCATCGATGTATGGCCTTG
37622 TGCATCGATGTATGGCCTTG
1 TGCATCGATGTATGGCCTTG
37642 TGCATCGATGTA
1 TGCATCGATGTA
37654 CATTCAAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (20 bp):
TGCATCGATGTATGGCCTTG
Found at i:37671 original size:23 final size:22
Alignment explanation
Indices: 37641--37722 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
37631 GTATGGCCTT
*
37641 GTGCATCGATGTACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
37663 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
37685 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
37708 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
37723 TGTTAAGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 18 0.38
24 12 0.26
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:40992 original size:16 final size:18
Alignment explanation
Indices: 40961--41002 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
40951 ATAAAGTTTT
*
40961 AAAGTTGTTATGCATT-A
1 AAAGTTGATATGCATTGA
40978 AAAGTTGATAT-CATTGA
1 AAAGTTGATATGCATTGA
*
40995 AAATTTGA
1 AAAGTTGA
41003 AATCTATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (18 bp):
AAAGTTGATATGCATTGA
Found at i:43288 original size:65 final size:64
Alignment explanation
Indices: 43155--43364 Score: 225
Period size: 65 Copynumber: 3.2 Consensus size: 64
43145 TGCACTAAGA
* * *
43155 GTGCATCGATGCATGAAATGCATTTC-ATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCA-TTCGATGTTTCATAAA-ATCCTGAGTGCATCGATGCATGG-T
43218 -T
63 AT
43219 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCTGAGTGCATCGATGCATGGTAT
* * ** *
43284 GTGCATCGATGCATAAAATACATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCC-TGAGTGCATCGATGCATGGTA
43346 TT
64 -T
*
43348 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
43365 CTTTGAACAA
Statistics
Matches: 128, Mismatches: 10, Indels: 15
0.84 0.07 0.10
Matches are distributed among these distances:
63 7 0.05
64 48 0.38
65 70 0.55
66 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCTGAGTGCATCGATGCATGGTAT
Done.