Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000912.1 Hibiscus syriacus cultivar Beakdansim tig00001815_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: 38322
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:2402 original size:2 final size:2
Alignment explanation
Indices: 2395--2427 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2385 TTACTATTAT
2395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2428 GAAAACGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11865 original size:21 final size:21
Alignment explanation
Indices: 11839--11880 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11829 CCATAATGGG
*
11839 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
11860 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
11881 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:11942 original size:21 final size:21
Alignment explanation
Indices: 11916--11959 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
11906 CTGTTGAACA
11916 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
11937 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
11958 GG
1 GG
11960 ACATTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:12010 original size:20 final size:20
Alignment explanation
Indices: 11985--12062 Score: 94
Period size: 20 Copynumber: 4.2 Consensus size: 20
11975 GCTTTAGACA
*
11985 GGGGGGAATCAGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
*
12005 GGGGGGTATCTGTA--CCC-
1 GGGGGGAATCTGTACCCCCT
*
12022 --GGGGTATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
12040 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
12060 GGG
1 GGG
12063 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
18 3 0.06
20 32 0.64
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:12027 original size:15 final size:15
Alignment explanation
Indices: 12007--12036 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11997 TACCCCCTGG
12007 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
12022 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
12037 CCTGGGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:12042 original size:35 final size:35
Alignment explanation
Indices: 11987--12056 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
11977 TTTAGACAGG
*
11987 GGGGAATCAGTACCCCCTGGGGGGTATCTGTACCC
1 GGGGAATCAGTACCCCCTGGGGGGAATCTGTACCC
* *
12022 GGGGTATCTGTACCCCCTGGGGGGAATCTGTACCC
1 GGGGAATCAGTACCCCCTGGGGGGAATCTGTACCC
12057 CCTGGGCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (35 bp):
GGGGAATCAGTACCCCCTGGGGGGAATCTGTACCC
Found at i:12401 original size:22 final size:22
Alignment explanation
Indices: 12370--12416 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
12360 AAGCTCCCCC
12370 TTTTTCATTAAGAAATTGAATT
1 TTTTTCATTAAGAAATTGAATT
*
12392 TTTTTTATTAAGAAATTGAATT
1 TTTTTCATTAAGAAATTGAATT
12414 TTT
1 TTT
12417 CAAACCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTTTCATTAAGAAATTGAATT
Found at i:14445 original size:34 final size:32
Alignment explanation
Indices: 14392--14461 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
14382 ACCTTACAAC
* *
14392 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
* *
14424 TCCCTAGCTTTTACACGGGCTAAGCTATAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
14458 TCCC
1 TCCC
14462 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:14771 original size:21 final size:21
Alignment explanation
Indices: 14745--14786 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
14735 CCAGAATGGG
*
14745 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
14766 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
14787 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:14848 original size:20 final size:20
Alignment explanation
Indices: 14823--14884 Score: 124
Period size: 20 Copynumber: 3.1 Consensus size: 20
14813 TGTTGAACAG
14823 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
14843 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
14863 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
14883 GG
1 GG
14885 ACATTCTGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.15, C:0.29, G:0.42, T:0.15
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:14936 original size:21 final size:21
Alignment explanation
Indices: 14910--14989 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
14900 GCTTTAGACA
*
14910 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
14931 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
14948 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
14967 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
14988 GG
1 GG
14990 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 32 0.64
ACGTcount: A:0.12, C:0.28, G:0.40, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:14951 original size:15 final size:15
Alignment explanation
Indices: 14933--14962 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14923 ACCCCCTGGG
14933 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
14948 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
14963 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:14968 original size:36 final size:36
Alignment explanation
Indices: 14912--14983 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
14902 TTTAGACAGG
*
14912 GGGGAATCGGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
* *
14948 GGGGTATCTGTACCCCCTGGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
14984 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.21
Consensus pattern (36 bp):
GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
Found at i:18729 original size:14 final size:16
Alignment explanation
Indices: 18708--18743 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
18698 GAAGTTGGTG
*
18708 GTTTTTTTTGGTTTT-
1 GTTTTTTATGGTTTTA
18723 GTTTTTTATGGTTTTA
1 GTTTTTTATGGTTTTA
18739 GTTTT
1 GTTTT
18744 CACAATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.06, C:0.00, G:0.19, T:0.75
Consensus pattern (16 bp):
GTTTTTTATGGTTTTA
Found at i:20181 original size:20 final size:21
Alignment explanation
Indices: 20143--20181 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20133 TTCTGATATG
*
20143 TTTTTTAATCTTTAGAACACT
1 TTTTTTAATCTTTACAACACT
*
20164 TTTTTTTATCTTT-CAACA
1 TTTTTTAATCTTTACAACA
20182 AATTTTCGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.15, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTTTTAATCTTTACAACACT
Found at i:21412 original size:16 final size:17
Alignment explanation
Indices: 21391--21442 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
21381 AAATTAATTT
21391 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
21407 AATTACTCATAA-TTT--
1 AATTACTC-TAACTTTCA
*
21422 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
21439 AATT
1 AATT
21443 TAAATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 10 0.34
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:26339 original size:109 final size:107
Alignment explanation
Indices: 26194--26400 Score: 265
Period size: 109 Copynumber: 1.9 Consensus size: 107
26184 GACACCTGTG
* * * * * *
26194 TCCAACTTCCAAGGACTCTCCGGACATATGGGAATCTTGGAAAAAAATTGAACACAT-C-TGTGT
1 TCCAACCTCCAAGGACTATCCGAACACATGGAAATCTTGGAAAAAAAATG--CACATGCTTGTGT
* *
26257 TGGACGCATACCCATTTTAGACATACACCTGAGTCCAGCACCCATA
64 TGGACACATACCCATGTTAGAC--ACACCTGAGTCCAGCACCCATA
* * *
26303 TCCAACCTCCAAGGACTATCCGAATACATGGAAATCTTGGAAAAAAAATGTATATGCTTGTGTTG
1 TCCAACCTCCAAGGACTATCCGAACACATGGAAATCTTGGAAAAAAAATGCACATGCTTGTGTTG
26368 GACACATACCCATGTTAGACACACCTGAGTCCA
66 GACACATACCCATGTTAGACACACCTGAGTCCA
26401 AGTAATTTAG
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 16 0.19
108 1 0.01
109 68 0.80
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (107 bp):
TCCAACCTCCAAGGACTATCCGAACACATGGAAATCTTGGAAAAAAAATGCACATGCTTGTGTTG
GACACATACCCATGTTAGACACACCTGAGTCCAGCACCCATA
Found at i:29196 original size:15 final size:15
Alignment explanation
Indices: 29163--29214 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
29153 TAAAAAATAT
*
29163 AAAAAATAAAATAAG
1 AAAAAATAAAATAAA
**
29178 AAAAAATAATGTAAA
1 AAAAAATAAAATAAA
29193 AAAAAGA-AAAATAAA
1 AAAAA-ATAAAATAAA
29208 ATAAAAA
1 A-AAAAA
29215 AACAAAAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 25 0.83
16 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAATAAA
Found at i:29222 original size:20 final size:19
Alignment explanation
Indices: 29165--29222 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
29155 AAAAATATAA
*
29165 AAAATAAAATAAGAAAAAAT
1 AAAATAAAA-AAAAAAAAAT
**
29185 AATGTAAAAAAAAGAAAAAT
1 AAAATAAAAAAAA-AAAAAT
*
29205 AAAATAAAAAAACAAAAA
1 AAAATAAAAAAAAAAAAA
29223 CCAAAACCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAATAAAAAAAAAAAAAT
Found at i:34196 original size:21 final size:21
Alignment explanation
Indices: 34172--34225 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
34162 GTTGTCGTAG
34172 TAATTCACAATATTAATATAA
1 TAATTCACAATATTAATATAA
* ** * *
34193 TAATTAACGGTGTTAATGTAA
1 TAATTCACAATATTAATATAA
*
34214 TAATCCACAATA
1 TAATTCACAATA
34226 ATTGATAATA
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.35
Consensus pattern (21 bp):
TAATTCACAATATTAATATAA
Found at i:35612 original size:19 final size:19
Alignment explanation
Indices: 35590--35626 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35580 CATCTTTAAA
*
35590 AAATAATTTTATTACTAAC
1 AAATAATTTAATTACTAAC
*
35609 AAATTATTTAATTACTAA
1 AAATAATTTAATTACTAA
35627 TTTTTTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATTTAATTACTAAC
Found at i:37519 original size:18 final size:18
Alignment explanation
Indices: 37479--37515 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
37469 TAATAGTGAG
37479 TTATTATAAAATATATTT
1 TTATTATAAAATATATTT
*
37497 TTATTAT-AATTATATTT
1 TTATTATAAAATATATTT
37514 TT
1 TT
37516 TATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATAAAATATATTT
Done.