Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003715.1 Hibiscus syriacus cultivar Beakdansim tig00007945_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: 98902
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3577 original size:20 final size:20
Alignment explanation
Indices: 3552--3590 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3542 GGTATTTTTC
3552 ATAATAATAATAACAATTTA
1 ATAATAATAATAACAATTTA
*
3572 ATAATAATAATAATAATTT
1 ATAATAATAATAACAATTT
3591 TAAACCCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAATAATAATAACAATTTA
Found at i:12336 original size:7 final size:7
Alignment explanation
Indices: 12324--12353 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
12314 GTAATCTTTC
12324 TTATTGG
1 TTATTGG
12331 TTATTGG
1 TTATTGG
12338 TTATTGG
1 TTATTGG
12345 TTATTGG
1 TTATTGG
12352 TT
1 TT
12354 GGCATGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (7 bp):
TTATTGG
Found at i:14281 original size:14 final size:15
Alignment explanation
Indices: 14253--14282 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14243 TGATATGCTC
14253 TGATATGATTTAATT
1 TGATATGATTTAATT
14268 TGATATGA-TTAATT
1 TGATATGATTTAATT
14282 T
1 T
14283 TTTTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
TGATATGATTTAATT
Found at i:15291 original size:3 final size:3
Alignment explanation
Indices: 15283--15313 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
15273 AAACACTTCC
15283 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
15314 CTTTTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:15709 original size:2 final size:2
Alignment explanation
Indices: 15702--15736 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15692 ATTTTGTCAT
15702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15737 TTGTATTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15833 original size:26 final size:26
Alignment explanation
Indices: 15785--15844 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
15775 ATGTATCGTA
*
15785 TATATATATATATATATTAATTTGATAT
1 TATATATATATATATATGAATTT--TAT
*
15813 TATATA-AT-TATATATGGATTTTAT
1 TATATATATATATATATGAATTTTAT
15837 TATATATA
1 TATATATA
15845 AATTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 9 0.31
25 1 0.03
26 11 0.38
27 2 0.07
28 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (26 bp):
TATATATATATATATATGAATTTTAT
Found at i:19508 original size:5 final size:5
Alignment explanation
Indices: 19498--19523 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19488 TTTTTAGTGT
19498 TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA T
19524 CCAACAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:24563 original size:14 final size:14
Alignment explanation
Indices: 24544--24579 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
24534 AATTCATTTA
24544 ATATATATATATAT
1 ATATATATATATAT
24558 ATATATAT-TATAT
1 ATATATATATATAT
24571 AT-TATATAT
1 ATATATATAT
24580 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 8 0.38
14 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:24580 original size:14 final size:15
Alignment explanation
Indices: 24544--24582 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
24534 AATTCATTTA
24544 ATATATA-TATATAT
1 ATATATATTATATAT
24558 ATATATATTATATAT
1 ATATATATTATATAT
24573 -TATATATTAT
1 ATATATATTAT
24583 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATATATTATATAT
Found at i:24594 original size:2 final size:2
Alignment explanation
Indices: 24544--24579 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
24534 AATTCATTTA
24544 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24580 TATTTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:27056 original size:22 final size:20
Alignment explanation
Indices: 27021--27060 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
27011 AACATTCGTT
27021 TTAGATTAATTGATAATAAA
1 TTAGATTAATTGATAATAAA
27041 TTAGATATAGATTGATAATA
1 TTAGAT-TA-ATTGATAATA
27061 TTATTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (20 bp):
TTAGATTAATTGATAATAAA
Found at i:36206 original size:32 final size:31
Alignment explanation
Indices: 36170--36231 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
36160 CCCGTGATTT
*
36170 AATTAACATACCTACCCA-AAACTCTAATTCAC
1 AATT-ACATACCGACCCACAAACTCT-ATTCAC
* *
36202 AATTACCTACCGATCCACAAACTCTATTCA
1 AATTACATACCGACCCACAAACTCTATTCA
36232 GCCAAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.40, C:0.32, G:0.02, T:0.26
Consensus pattern (31 bp):
AATTACATACCGACCCACAAACTCTATTCAC
Found at i:36871 original size:2 final size:2
Alignment explanation
Indices: 36864--36889 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36854 ACGAGAGCCT
36864 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
36890 AACAAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42651 original size:38 final size:38
Alignment explanation
Indices: 42577--42651 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
42567 TTATATTTTC
*
42577 AATTTTGTAAAAAAAATTATATAAATTTTATGAATTTA
1 AATTTTGTAAAAAAAATTATATAAATTTTATCAATTTA
* * *
42615 AATTTTTTAAAGAAAA-TATATAAATATTTTTCAATTT
1 AATTTTGTAAAAAAAATTATATAAAT-TTTATCAATTT
42652 GTTAAAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 9 0.28
38 23 0.72
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (38 bp):
AATTTTGTAAAAAAAATTATATAAATTTTATCAATTTA
Found at i:44258 original size:3 final size:3
Alignment explanation
Indices: 44250--44281 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
44240 TATTCAAAAT
44250 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
44282 TATAAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:49539 original size:31 final size:31
Alignment explanation
Indices: 49504--49591 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
49494 ACATGTTATC
*
49504 ACTTTCAACACGTGATATATACCACATCATT
1 ACTTTCAACACGTGATATATACCACATCATA
** * * * *
49535 ACTTTTTATATGTGGTATATACCACGTCATA
1 ACTTTCAACACGTGATATATACCACATCATA
* * *
49566 ATTTTCGACACGTGATATGTACCACA
1 ACTTTCAACACGTGATATATACCACA
49592 CTATCATTTT
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (31 bp):
ACTTTCAACACGTGATATATACCACATCATA
Found at i:49730 original size:31 final size:31
Alignment explanation
Indices: 49695--49764 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
49685 CACCACTTTC
* *
49695 GATATGTACCAAGTGATCACTTTTAACACAT
1 GATATATACCAAGTAATCACTTTTAACACAT
* *
49726 GATATATACCACGTAATCTCTTTTAACACAT
1 GATATATACCAAGTAATCACTTTTAACACAT
49757 GATATATA
1 GATATATA
49765 TTACATATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (31 bp):
GATATATACCAAGTAATCACTTTTAACACAT
Found at i:61499 original size:3 final size:3
Alignment explanation
Indices: 61491--61524 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
61481 TATATATATA
61491 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
61525 GGGAAAAAAA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:79261 original size:20 final size:22
Alignment explanation
Indices: 79222--79261 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
79212 GGCTTTAGCT
*
79222 AAGCATAATGCATTGATTGTCG
1 AAGCATAATGCATAGATTGTCG
79244 AAGCAT-ATGC-TAGATTGT
1 AAGCATAATGCATAGATTGT
79262 TAATAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (22 bp):
AAGCATAATGCATAGATTGTCG
Found at i:92018 original size:20 final size:21
Alignment explanation
Indices: 91993--92031 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
91983 GGCTGCTGGA
91993 AATCGGTT-TAACCGGTTTTC
1 AATCGGTTCTAACCGGTTTTC
*
92013 AATCGGTTCTGACCGGTTT
1 AATCGGTTCTAACCGGTTT
92032 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (21 bp):
AATCGGTTCTAACCGGTTTTC
Found at i:92068 original size:49 final size:50
Alignment explanation
Indices: 92002--92106 Score: 135
Period size: 49 Copynumber: 2.1 Consensus size: 50
91992 AAATCGGTTT
* *
92002 AACCGGTTTTCAATCGGTTCT-GACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTTCAATCGG-TCTAAACCGGTTTGACCGGTCTCAACCGGTTCG
* * *
92052 AACCGGTTTT-GATCGGTCTAAACCGGTTTGACCGGTCTGAACCGGTTTG
1 AACCGGTTTTCAATCGGTCTAAACCGGTTTGACCGGTCTCAACCGGTTCG
92101 -ACCGGT
1 AACCGGT
92107 CTGACCCGAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 9 0.18
49 30 0.61
50 10 0.20
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (50 bp):
AACCGGTTTTCAATCGGTCTAAACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:92107 original size:19 final size:19
Alignment explanation
Indices: 92016--92110 Score: 104
Period size: 19 Copynumber: 4.9 Consensus size: 19
92006 GGTTTTCAAT
*
92016 CGGTTCTGACCGGTTTG-AC
1 CGGTT-TGACCGGTCTGAAC
*
92035 CGGTTTCAACCGGT-TCGAAC
1 CGGTTT-GACCGGTCT-GAAC
* *
92055 CGGTTTTGATCGGTCTAAAC
1 CGG-TTTGACCGGTCTGAAC
92075 CGGTTTGACCGGTCTGAAC
1 CGGTTTGACCGGTCTGAAC
92094 CGGTTTGACCGGTCTGA
1 CGGTTTGACCGGTCTGA
92111 CCCGACCCGA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
18 2 0.03
19 43 0.66
20 16 0.25
21 4 0.06
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.29
Consensus pattern (19 bp):
CGGTTTGACCGGTCTGAAC
Found at i:92111 original size:9 final size:9
Alignment explanation
Indices: 92073--92112 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
92063 ATCGGTCTAA
*
92073 ACCGGTTTG
1 ACCGGTCTG
92082 ACCGGTCTG
1 ACCGGTCTG
*
92091 AACCGGTTTG
1 -ACCGGTCTG
92101 ACCGGTCTG
1 ACCGGTCTG
92110 ACC
1 ACC
92113 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:92130 original size:17 final size:17
Alignment explanation
Indices: 92108--92163 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
92098 TTGACCGGTC
92108 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
92125 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
92142 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
92159 TGACC
1 TGACC
92164 GTTGACTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:98622 original size:30 final size:29
Alignment explanation
Indices: 98586--98642 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
98576 GTTTAACGGT
*
98586 TTTCAACCGGTTCTGACCGGTTTTGACCAG
1 TTTCAACCGGTTC-GAACGGTTTTGACCAG
98616 TTTCAACCGGTTCGAACGGTTTTGACC
1 TTTCAACCGGTTCGAACGGTTTTGACC
98643 TGTCTGAACG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (29 bp):
TTTCAACCGGTTCGAACGGTTTTGACCAG
Found at i:98666 original size:17 final size:19
Alignment explanation
Indices: 98629--98666 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
98619 CAACCGGTTC
*
98629 GAACGGTTTTGACCTGTCT
1 GAACGGTTTTGACCGGTCT
98648 GAACGG-TTTGA-CGGTCT
1 GAACGGTTTTGACCGGTCT
98665 GA
1 GA
98667 CCCGACCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 5 0.28
19 6 0.33
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (19 bp):
GAACGGTTTTGACCGGTCT
Found at i:98697 original size:19 final size:19
Alignment explanation
Indices: 98668--98720 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
98658 ACGGTCTGAC
98668 CCGACCGACCGTTGACCCGA
1 CCGA-CGACCGTTGACCCGA
98688 CCGACGACCGTTGACCCGA
1 CCGACGACCGTTGACCCGA
*
98707 CC--CGACCGCTGACC
1 CCGACGACCGTTGACC
98721 GTTGACTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 11 0.34
19 17 0.53
20 4 0.12
ACGTcount: A:0.19, C:0.47, G:0.25, T:0.09
Consensus pattern (19 bp):
CCGACGACCGTTGACCCGA
Found at i:98710 original size:24 final size:24
Alignment explanation
Indices: 98681--98726 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
98671 ACCGACCGTT
98681 GACCCGACCGAC-GACCGTTGACCC
1 GACCCGACCG-CTGACCGTTGACCC
98705 GACCCGACCGCTGACCGTTGAC
1 GACCCGACCGCTGACCGTTGAC
98727 TTTCTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.20, C:0.43, G:0.26, T:0.11
Consensus pattern (24 bp):
GACCCGACCGCTGACCGTTGACCC
Done.