Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007784.1 Hibiscus syriacus cultivar Beakdansim tig00110069_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: 72309
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2741 original size:11 final size:11
Alignment explanation
Indices: 2725--2756 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
2715 CGTCATATAT
2725 AGCTCACAAAC
1 AGCTCACAAAC
2736 AGCTCACAAAC
1 AGCTCACAAAC
2747 AGCTCACAAA
1 AGCTCACAAA
2757 GTACAAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.34, G:0.09, T:0.09
Consensus pattern (11 bp):
AGCTCACAAAC
Found at i:9690 original size:21 final size:21
Alignment explanation
Indices: 9664--9718 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
9654 AATTCAGAGA
9664 TATTACGAAGGTACTCCATCC
1 TATTACGAAGGTACTCCATCC
* *
9685 TATTACAAAGGTACTTCATCC
1 TATTACGAAGGTACTCCATCC
9706 TATTACGAAGGTA
1 TATTACGAAGGTA
9719 ATCCTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (21 bp):
TATTACGAAGGTACTCCATCC
Found at i:12604 original size:14 final size:14
Alignment explanation
Indices: 12585--12622 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
12575 TGATTGATCT
12585 CCCTCCTAGTCGAG
1 CCCTCCTAGTCGAG
12599 CCCTCCTA-TCGAG
1 CCCTCCTAGTCGAG
* *
12612 ACTTCCTAGTC
1 CCCTCCTAGTC
12623 TCAATGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.16, C:0.42, G:0.16, T:0.26
Consensus pattern (14 bp):
CCCTCCTAGTCGAG
Found at i:19709 original size:13 final size:13
Alignment explanation
Indices: 19687--19716 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19677 ACTAAACACC
19687 TTTC-ACATACCT
1 TTTCAACATACCT
19699 TTTCAACATACCT
1 TTTCAACATACCT
19712 TTTCA
1 TTTCA
19717 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:22572 original size:24 final size:24
Alignment explanation
Indices: 22545--22593 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
22535 TTCCACCAAA
*
22545 GCTT-TGATTACCGCTTGATGTAAG
1 GCTTCTGA-TACCACTTGATGTAAG
*
22569 GCTTCTGATGCCACTTGATGTAAG
1 GCTTCTGATACCACTTGATGTAAG
22593 G
1 G
22594 AACTTGTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (24 bp):
GCTTCTGATACCACTTGATGTAAG
Found at i:24297 original size:36 final size:35
Alignment explanation
Indices: 24247--24315 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
24237 CCTAAACATC
* *
24247 ACCATCTTCCATCACCATTTTCACGCCTATATAATT
1 ACCATATTCCATCACCA-TTTCACGCCTAAATAATT
*
24283 ACCATATTCTATCACCATTTCACGCCTAAATAA
1 ACCATATTCCATCACCATTTCACGCCTAAATAA
24316 CCACCACTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.33
Consensus pattern (35 bp):
ACCATATTCCATCACCATTTCACGCCTAAATAATT
Found at i:30596 original size:9 final size:9
Alignment explanation
Indices: 30582--30648 Score: 59
Period size: 9 Copynumber: 7.7 Consensus size: 9
30572 TATTTTTTTC
30582 AAAAAAACA
1 AAAAAAACA
*
30591 AAAAAACCA
1 AAAAAAACA
**
30600 AAAAAGGCA
1 AAAAAAACA
*
30609 AAAAAAGGC-
1 AAAAAA-ACA
30618 -AAAAAA-A
1 AAAAAAACA
*
30625 AAAAAAGCA
1 AAAAAAACA
30634 AAAAAAACA
1 AAAAAAACA
30643 AAAAAA
1 AAAAAA
30649 GAGCCAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
8 10 0.21
9 35 0.74
10 2 0.04
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:30613 original size:11 final size:10
Alignment explanation
Indices: 30599--30666 Score: 58
Period size: 9 Copynumber: 7.3 Consensus size: 10
30589 CAAAAAAACC
30599 AAAAAAGGCA
1 AAAAAAGGCA
30609 AAAAAAGGC-
1 AAAAAAGGCA
30618 AAAAAA---A
1 AAAAAAGGCA
30625 AAAAAA-GCA
1 AAAAAAGGCA
*
30634 AAAAAA-ACA
1 AAAAAAGGCA
*
30643 AAAAAAGAGCC
1 AAAAAAG-GCA
*
30654 AAAAAAGCCA
1 AAAAAAGGCA
30664 AAA
1 AAA
30667 TTTCAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
7 6 0.12
9 21 0.44
10 13 0.27
11 8 0.17
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGGCA
Found at i:30626 original size:15 final size:15
Alignment explanation
Indices: 30583--30646 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 15
30573 ATTTTTTTCA
*
30583 AAAAAACAAAAAAACC
1 AAAAAA-AAAAAAAGC
30599 AAAAAAGGCAAAAAAAGGC
1 AAAAAA---AAAAAAA-GC
30618 AAAAAAAAAAAAAGC
1 AAAAAAAAAAAAAGC
30633 AAAAAAAACAAAAA
1 AAAAAAAA-AAAAA
30647 AAGAGCCAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
15 10 0.23
16 18 0.42
18 8 0.19
19 7 0.16
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGC
Found at i:30628 original size:34 final size:35
Alignment explanation
Indices: 30583--30659 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 35
30573 ATTTTTTTCA
**
30583 AAAAAACAAAAAAACCAAAAAAGGCAAAAAAAG-GC
1 AAAAAA-AAAAAAACCAAAAAAAACAAAAAAAGAGC
*
30618 AAAAAAAAAAAAAGCAAAAAAAACAAAAAAAGAGC
1 AAAAAAAAAAAAACCAAAAAAAACAAAAAAAGAGC
*
30653 CAAAAAA
1 AAAAAAA
30660 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 23 0.62
35 14 0.38
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (35 bp):
AAAAAAAAAAAAACCAAAAAAAACAAAAAAAGAGC
Found at i:30657 original size:9 final size:9
Alignment explanation
Indices: 30589--30666 Score: 52
Period size: 9 Copynumber: 8.6 Consensus size: 9
30579 TTCAAAAAAA
*
30589 CAAAAAAAC
1 CAAAAAAGC
30598 CAAAAAAGGC
1 CAAAAAA-GC
* *
30608 AAAAAAAGG
1 CAAAAAAGC
30617 CAAAAAA--
1 CAAAAAAGC
*
30624 AAAAAAAGC
1 CAAAAAAGC
* *
30633 AAAAAAAAC
1 CAAAAAAGC
*
30642 AAAAAAAGAGC
1 -CAAAAA-AGC
30653 CAAAAAAGC
1 CAAAAAAGC
30662 CAAAA
1 CAAAA
30667 TTTCAAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
7 6 0.11
9 30 0.54
10 18 0.32
11 2 0.04
ACGTcount: A:0.76, C:0.14, G:0.10, T:0.00
Consensus pattern (9 bp):
CAAAAAAGC
Found at i:40925 original size:13 final size:13
Alignment explanation
Indices: 40907--40941 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
40897 TCATTCCATG
40907 CACAAGGCTGCAC
1 CACAAGGCTGCAC
40920 CACAAGGCTGCAC
1 CACAAGGCTGCAC
40933 CACAAGGCT
1 CACAAGGCT
40942 TCCTAGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.37, G:0.23, T:0.09
Consensus pattern (13 bp):
CACAAGGCTGCAC
Found at i:41829 original size:16 final size:16
Alignment explanation
Indices: 41804--41834 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41794 AAGTGCAAAG
*
41804 TCAAAGAAAAAGAAAA
1 TCAAAAAAAAAGAAAA
41820 TCAAAAAAAAAGAAA
1 TCAAAAAAAAAGAAA
41835 TTGAAGCACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.06, G:0.10, T:0.06
Consensus pattern (16 bp):
TCAAAAAAAAAGAAAA
Found at i:41870 original size:28 final size:26
Alignment explanation
Indices: 41822--41887 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
41812 AAAGAAAATC
*
41822 AAAAAA-AAAGAAATTGAAGCACTCCA
1 AAAAAAGAAAGAAATTCAAGCACT-CA
* *
41848 AAAGAAAGAAAGAAATTCCAGCACTTA
1 AAA-AAAGAAAGAAATTCAAGCACTCA
41875 AAAAAAG-AAGAAA
1 AAAAAAGAAAGAAA
41888 AGCAAAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 6 0.17
26 7 0.20
27 7 0.20
28 15 0.43
ACGTcount: A:0.64, C:0.12, G:0.14, T:0.11
Consensus pattern (26 bp):
AAAAAAGAAAGAAATTCAAGCACTCA
Found at i:46451 original size:180 final size:180
Alignment explanation
Indices: 46149--46508 Score: 720
Period size: 180 Copynumber: 2.0 Consensus size: 180
46139 TGAAGGTTAA
46149 TGAACATGTTCTTTATAATTTCAACTAACACGTCTTTTGGAATTTCAAAAGATATGATGCTTGAA
1 TGAACATGTTCTTTATAATTTCAACTAACACGTCTTTTGGAATTTCAAAAGATATGATGCTTGAA
46214 TCATCTTGAATGTCCCTTGGAATAACCTGCAAATTCAAAGAATGAATAGAAGAAAAAAATTGATT
66 TCATCTTGAATGTCCCTTGGAATAACCTGCAAATTCAAAGAATGAATAGAAGAAAAAAATTGATT
46279 AGTATAAAGCAAACCTTCCTTTTCCTCGCACTCTTTTCATTCATGCTCAT
131 AGTATAAAGCAAACCTTCCTTTTCCTCGCACTCTTTTCATTCATGCTCAT
46329 TGAACATGTTCTTTATAATTTCAACTAACACGTCTTTTGGAATTTCAAAAGATATGATGCTTGAA
1 TGAACATGTTCTTTATAATTTCAACTAACACGTCTTTTGGAATTTCAAAAGATATGATGCTTGAA
46394 TCATCTTGAATGTCCCTTGGAATAACCTGCAAATTCAAAGAATGAATAGAAGAAAAAAATTGATT
66 TCATCTTGAATGTCCCTTGGAATAACCTGCAAATTCAAAGAATGAATAGAAGAAAAAAATTGATT
46459 AGTATAAAGCAAACCTTCCTTTTCCTCGCACTCTTTTCATTCATGCTCAT
131 AGTATAAAGCAAACCTTCCTTTTCCTCGCACTCTTTTCATTCATGCTCAT
46509 GTTTTTCAAC
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 180 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (180 bp):
TGAACATGTTCTTTATAATTTCAACTAACACGTCTTTTGGAATTTCAAAAGATATGATGCTTGAA
TCATCTTGAATGTCCCTTGGAATAACCTGCAAATTCAAAGAATGAATAGAAGAAAAAAATTGATT
AGTATAAAGCAAACCTTCCTTTTCCTCGCACTCTTTTCATTCATGCTCAT
Found at i:59330 original size:91 final size:91
Alignment explanation
Indices: 59175--59357 Score: 303
Period size: 91 Copynumber: 2.0 Consensus size: 91
59165 GGTAGTTGAT
*
59175 GCTTGGCCGAATAGGGAGTGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
*
59240 GGGGCTGATCACATGCAAAACACATG
66 GAGGCTGATCACATGCAAAACACATG
*
59266 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
* * **
59331 GAGGCTGGTCATATGCAAGGCACATG
66 GAGGCTGATCACATGCAAAACACATG
59357 G
1 G
59358 GTATTCTAGG
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
GAGGCTGATCACATGCAAAACACATG
Found at i:61092 original size:24 final size:21
Alignment explanation
Indices: 61057--61099 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
61047 GGCACATTCT
*
61057 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
61080 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
61100 GTCTTGTGGA
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:63550 original size:22 final size:18
Alignment explanation
Indices: 63504--63547 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
63494 GTCTCATTCA
63504 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
63522 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
63540 AGCTAGCT
1 AGCTAGCT
63548 AGCAAACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (18 bp):
AGCTAGCTTGAGTTGTGG
Done.