Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002084.1 Hibiscus syriacus cultivar Beakdansim tig00004256_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: 65722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1879 original size:3 final size:3
Alignment explanation
Indices: 1871--1911 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1861 TGTTATTTTC
1871 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1912 GTGTCCTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2894 original size:20 final size:20
Alignment explanation
Indices: 2857--2905 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
2847 TATTAAGAAA
*
2857 ATAAAATAAATTAATAAA-AT
1 ATAAAA-AAAATAATAAATAT
2877 ATAAAAAAAATAATTAAATTAT
1 ATAAAAAAAATAA-TAAA-TAT
2899 ATAAAAA
1 ATAAAAA
2906 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
22 9 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAAAAAATAATAAATAT
Found at i:2895 original size:19 final size:20
Alignment explanation
Indices: 2857--2905 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
2847 TATTAAGAAA
*
2857 ATAAAATAAATTAATAAAA-T
1 ATAAAA-AAAATAATAAAATT
*
2877 ATAAAAAAAATAATTAAATT
1 ATAAAAAAAATAATAAAATT
2897 ATATAAAAA
1 ATA-AAAAA
2906 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 10 0.40
21 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAAAAAATAATAAAATT
Found at i:2912 original size:28 final size:29
Alignment explanation
Indices: 2844--2912 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 29
2834 AATGTAATTT
2844 ATATATTAAGAAAATAAAATAAATTAATAAA
1 ATAT-TTAA-AAAATAAAATAAATTAATAAA
** *
2875 ATATAAAAAAAAT-AATTAAATTATATAAA
1 ATATTTAAAAAATAAAATAAATTA-ATAAA
2904 A-ATTTAAAA
1 ATATTTAAAA
2913 TTTTAAAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 15 0.47
29 11 0.34
30 2 0.06
31 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (29 bp):
ATATTTAAAAAATAAAATAAATTAATAAA
Found at i:3674 original size:16 final size:16
Alignment explanation
Indices: 3640--3680 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3630 GTTTATTTTA
*
3640 GAATGATT-AAACGTT
1 GAATGATTCAAACATT
*
3655 GAATGATTCAAATATT
1 GAATGATTCAAACATT
3671 GAATGATTCA
1 GAATGATTCA
3681 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAACATT
Found at i:5421 original size:29 final size:29
Alignment explanation
Indices: 5388--5445 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5378 ATCATTATCC
5388 ATTCAATGGGCTTTCTTCCCAATCAACAT
1 ATTCAATGGGCTTTCTTCCCAATCAACAT
5417 ATTCAATGGGCTTTCTTCCCAATCAACAT
1 ATTCAATGGGCTTTCTTCCCAATCAACAT
5446 CAATCTTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (29 bp):
ATTCAATGGGCTTTCTTCCCAATCAACAT
Found at i:6004 original size:25 final size:25
Alignment explanation
Indices: 5976--6060 Score: 118
Period size: 25 Copynumber: 3.4 Consensus size: 25
5966 TGTACAATAT
* *
5976 TTTTAAAAGTTCGTTTTTACGACAC
1 TTTTAAAAGTTCGTTTCTACAACAC
6001 TTTTAAAAGTTCGTTTCTACAACAC
1 TTTTAAAAGTTCGTTTCTACAACAC
*
6026 TTTTAAAAGTTCGTTGC-ATCAACAC
1 TTTTAAAAGTTCGTTTCTA-CAACAC
*
6051 TTTTACAAGT
1 TTTTAAAAGT
6061 CACTATACCA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 1 0.02
25 54 0.98
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.41
Consensus pattern (25 bp):
TTTTAAAAGTTCGTTTCTACAACAC
Found at i:8069 original size:60 final size:60
Alignment explanation
Indices: 7988--8352 Score: 452
Period size: 60 Copynumber: 6.1 Consensus size: 60
7978 ACGTCTTTCA
* *
7988 TTGGCTTCAG-TCCAGCATCCTTCTTCGGCTTTAATTCCTCCTCATAGATCATATCCTTAT
1 TTGGCTTCAGCT-CTGCATCCTTCTTCGGCTTTAATTCCTCCTCATAGATCATATCCTTAC
* *
8048 TTGGTTTCAGTTCTGCATCCTTCTTCGGCTTTAATTCCTCCTCATAGATCATATCCTTAC
1 TTGGCTTCAGCTCTGCATCCTTCTTCGGCTTTAATTCCTCCTCATAGATCATATCCTTAC
* * * * * * *
8108 TTGGTTTCGGTTCTGCTTCCTTCATT-GGCTTTAATGT-CTCCTTATAGAGCTTATCCTTAC
1 TTGGCTTCAGCTCTGCATCCTTC-TTCGGCTTTAAT-TCCTCCTCATAGATCATATCCTTAC
* * *
8168 TTGGCTTCAGCTCTGTATCCTTCTTTGGCTTTAATTCCTCCTCATAG-TACGTATCCTTAC
1 TTGGCTTCAGCTCTGCATCCTTCTTCGGCTTTAATTCCTCCTCATAGAT-CATATCCTTAC
* * * *
8228 TTGGCTTCAGCTCTGCTTCCTTCTTCGGCTTTAATTCCTCCTCAAAAAACATATCCTTAC
1 TTGGCTTCAGCTCTGCATCCTTCTTCGGCTTTAATTCCTCCTCATAGATCATATCCTTAC
* * * *
8288 TTGGATTCAGCTCTGCATCCGTCTTCGGCTTTAATTCCTCCTCATA-ATACGTATCCTTCC
1 TTGGCTTCAGCTCTGCATCCTTCTTCGGCTTTAATTCCTCCTCATAGAT-CATATCCTTAC
8348 TTGGC
1 TTGGC
8353 CTCCAATCTA
Statistics
Matches: 266, Mismatches: 31, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
59 4 0.02
60 258 0.97
61 4 0.02
ACGTcount: A:0.16, C:0.29, G:0.13, T:0.42
Consensus pattern (60 bp):
TTGGCTTCAGCTCTGCATCCTTCTTCGGCTTTAATTCCTCCTCATAGATCATATCCTTAC
Found at i:10814 original size:2 final size:2
Alignment explanation
Indices: 10803--10853 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
10793 AATCTCCGGC
10803 AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG ACG A- AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG
*
10843 A- AG GG AG AG AG
1 AG AG AG AG AG AG
10854 TATTTATAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
1 4 0.10
2 36 0.86
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14127 original size:38 final size:38
Alignment explanation
Indices: 14072--14147 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
14062 AGTAGTACGA
*
14072 CAGGCTCCATCAGTATTTAATTTGAGCCAACCATTAGG
1 CAGGCTCCATCAGTATTTAATTTGAACCAACCATTAGG
* *
14110 CAGGCTCCGTC-GATATTTAATTTGAACGAACCATTAGG
1 CAGGCTCCATCAG-TATTTAATTTGAACCAACCATTAGG
14148 TGGGAGGGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (38 bp):
CAGGCTCCATCAGTATTTAATTTGAACCAACCATTAGG
Found at i:23291 original size:30 final size:29
Alignment explanation
Indices: 23255--23312 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
23245 TGATTTTTTC
*
23255 TGTTA-TTTACATTTCTGCCCTTTAAATTTA
1 TGTTATTTTA-ATTTCAG-CCTTTAAATTTA
23285 TGTTATTTTAATTTCAGCCTTTAAATTT
1 TGTTATTTTAATTTCAGCCTTTAAATTT
23313 CAGTCCTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 11 0.42
31 4 0.15
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (29 bp):
TGTTATTTTAATTTCAGCCTTTAAATTTA
Found at i:23322 original size:15 final size:15
Alignment explanation
Indices: 23294--23341 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
23284 ATGTTATTTT
23294 AATTTCAG-CCTTTA
1 AATTTCAGTCCTTTA
23308 AATTTCAGTCCTTTA
1 AATTTCAGTCCTTTA
*
23323 TATTTCAGTCCTTTA
1 AATTTCAGTCCTTTA
23338 AATT
1 AATT
23342 CTAGCTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (15 bp):
AATTTCAGTCCTTTA
Found at i:23351 original size:29 final size:28
Alignment explanation
Indices: 23273--23355 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
23263 ACATTTCTGC
*
23273 CCTTTAAATTT-ATGTTATTTTAATTTCAG
1 CCTTTAAATTTCA-G-TCTTTTAATTTCAG
*
23302 CCTTTAAATTTCAGTCCTTTATATTTCAG
1 CCTTTAAATTTCAGTCTTTTA-ATTTCAG
23331 TCCTTTAAA-TTCTAG-CTTTTAATTT
1 -CCTTTAAATTTC-AGTCTTTTAATTT
23356 TCTGAATTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 9 0.19
29 27 0.57
30 11 0.23
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (28 bp):
CCTTTAAATTTCAGTCTTTTAATTTCAG
Found at i:38227 original size:21 final size:21
Alignment explanation
Indices: 38198--38253 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
38188 TGCATTTTTT
*
38198 TTTAGAAAAATGATCGATCCC
1 TTTATAAAAATGATCGATCCC
38219 TTTATAAAAATGATCGATCCC
1 TTTATAAAAATGATCGATCCC
*
38240 TTTTTAAAAATGAT
1 TTTATAAAAATGAT
38254 AAATCCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (21 bp):
TTTATAAAAATGATCGATCCC
Found at i:40373 original size:17 final size:16
Alignment explanation
Indices: 40342--40379 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
40332 ACACTTTTAA
40342 TAAAA-ATATAAAATT
1 TAAAATATATAAAATT
40357 TAAAATATATAAAAATT
1 TAAAATATAT-AAAATT
40374 TAAAAT
1 TAAAAT
40380 TTTCAAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATATATAAAATT
Found at i:42375 original size:16 final size:17
Alignment explanation
Indices: 42343--42376 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42333 GCTACTCGAT
*
42343 TTTTTATTTTATTATTC
1 TTTTTATTTTATAATTC
42360 TTTTTATTTT-TAATTC
1 TTTTTATTTTATAATTC
42376 T
1 T
42377 CAAATTATTT
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:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTATAATTC
Found at i:47722 original size:19 final size:20
Alignment explanation
Indices: 47683--47723 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
47673 TTTGGAATCG
*
47683 GTTTTGAAGCTGAAGATGTTT
1 GTTTTGAAGCTG-ACATGTTT
47704 GTTTTGAAGCTG-CATGTTT
1 GTTTTGAAGCTGACATGTTT
47723 G
1 G
47724 GTAATTGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.20, C:0.07, G:0.29, T:0.44
Consensus pattern (20 bp):
GTTTTGAAGCTGACATGTTT
Found at i:53788 original size:4 final size:4
Alignment explanation
Indices: 53779--53805 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53769 CGTTAAATTA
53779 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
53806 AAATAGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:59661 original size:6 final size:6
Alignment explanation
Indices: 59650--59675 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
59640 TGATATCATC
59650 TACATA TACATA TACATA TACATA TA
1 TACATA TACATA TACATA TACATA TA
59676 AAATAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TACATA
Found at i:63464 original size:41 final size:42
Alignment explanation
Indices: 63389--63470 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 42
63379 GTGATTTCAC
63389 AAAGGTGAACAAACTTTAAAATCAGGTCAGGGATTAACTAAT
1 AAAGGTGAACAAACTTTAAAATCAGGTCAGGGATTAACTAAT
63431 AAAGGTGAACAAACTTT-AAATCAGGTCAGGGATTAACTAA
1 AAAGGTGAACAAACTTTAAAATCAGGTCAGGGATTAACTAA
63471 AATCAGGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 23 0.57
42 17 0.43
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAGGTGAACAAACTTTAAAATCAGGTCAGGGATTAACTAAT
Done.