Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008660.1 Hibiscus syriacus cultivar Beakdansim tig00111657_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: 1057077
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 5 of 5
Found at i:1031237 original size:16 final size:16
Alignment explanation
Indices: 1031213--1031257 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1031203 ATTAAAGTAT
*
1031213 TGGTTCTCATCGTTAG
1 TGGTGCTCATCGTTAG
1031229 TGGTGCTCATCGTTAG
1 TGGTGCTCATCGTTAG
*
1031245 TGTTGCTCATCGT
1 TGGTGCTCATCGT
1031258 GGTCGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.11, C:0.20, G:0.27, T:0.42
Consensus pattern (16 bp):
TGGTGCTCATCGTTAG
Found at i:1036429 original size:3 final size:3
Alignment explanation
Indices: 1036410--1036466 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
1036400 TATATAAATA
*
1036410 AAT ATT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT
*
1036456 AAC AAT AAT AA
1 AAT AAT AAT AA
1036467 GTTAGACCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 39 0.81
4 7 0.15
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1036466 original size:23 final size:22
Alignment explanation
Indices: 1036394--1036463 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
1036384 TTTCAGACCT
*
1036394 ATAAAATATATAAATAAATATTA
1 ATAAAATA-ATAAATAAATAATA
1036417 ATAAAATAAT-AAT-AATAATA
1 ATAAAATAATAAATAAATAATA
*
1036437 ATAATAATAATAAATAAATAACA
1 ATAA-AATAATAAATAAATAATA
1036460 ATAA
1 ATAA
1036464 TAAGTTAGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.24
21 9 0.21
22 5 0.12
23 18 0.43
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAAATAATAAATAAATAATA
Found at i:1036884 original size:97 final size:97
Alignment explanation
Indices: 1036717--1036896 Score: 263
Period size: 97 Copynumber: 1.9 Consensus size: 97
1036707 ATGACACTGC
* *
1036717 TCCTACGTGATGAGGAGATTTGGTCGGTGAACGACATTGTTCCTACATGAAGATAACGTCTAGTC
1 TCCTACGTGATGAGGAGATTTGGTCGGTGAACGACATTGTTCCTACATGAAGAGAACGTCTAGCC
*
1036782 GTCTTTAGGGACAATTTGGGAGACAACATGGT
66 ATCTTTAGGGACAATTTGGGAGACAACATGGT
* * * * *
1036814 TCCTATGTGATGAGGA-AGTTTGGTCGGTGGATGACATTGTTCCTACATGATGAGGACGTCTAGC
1 TCCTACGTGATGAGGAGA-TTTGGTCGGTGAACGACATTGTTCCTACATGAAGAGAACGTCTAGC
*
1036878 CATCTTTAGGGATAATTTG
65 CATCTTTAGGGACAATTTG
1036897 TTTCAAGAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 1 0.01
97 72 0.99
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (97 bp):
TCCTACGTGATGAGGAGATTTGGTCGGTGAACGACATTGTTCCTACATGAAGAGAACGTCTAGCC
ATCTTTAGGGACAATTTGGGAGACAACATGGT
Found at i:1036934 original size:34 final size:34
Alignment explanation
Indices: 1036891--1037017 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
1036881 CTTTAGGGAT
*
1036891 AATTTGTTTCAAGAGAAACTGTCTCAAGCGAGAC
1 AATTTGTTTCAAGAGAAACAGTCTCAAGCGAGAC
* * **
1036925 AATTTGTTTCAAGGGAAACAATCTCAA--TTG-C
1 AATTTGTTTCAAGAGAAACAGTCTCAAGCGAGAC
1036956 --TTATGTTTCAAGAGAAACAGTCTCAAGCGAGAC
1 AATT-TGTTTCAAGAGAAACAGTCTCAAGCGAGAC
* * *
1036989 AAAATTTGCTTCAAGGGAAACAATCTCAA
1 --AATTTGTTTCAAGAGAAACAGTCTCAA
1037018 AGGTTTATGT
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
29 2 0.03
30 21 0.29
31 1 0.01
32 2 0.03
33 1 0.01
34 24 0.33
36 20 0.27
37 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (34 bp):
AATTTGTTTCAAGAGAAACAGTCTCAAGCGAGAC
Found at i:1037147 original size:37 final size:36
Alignment explanation
Indices: 1037092--1037169 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 36
1037082 CAATTGTTTA
* *
1037092 TGTTTAAAGAGAATCTGTCTTAAG-AGAAACAAAACTT
1 TGTTTAAAGAGAAACTGTCTCAAGCA-AAACAAAA-TT
* *
1037129 TGTTTCAAGAGAAACTGTCTCAAGCAAGACAAAATT
1 TGTTTAAAGAGAAACTGTCTCAAGCAAAACAAAATT
1037165 TGTTT
1 TGTTT
1037170 TTAAGAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 7 0.19
37 28 0.78
38 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.31
Consensus pattern (36 bp):
TGTTTAAAGAGAAACTGTCTCAAGCAAAACAAAATT
Found at i:1037151 original size:67 final size:66
Alignment explanation
Indices: 1036895--1037143 Score: 322
Period size: 67 Copynumber: 3.8 Consensus size: 66
1036885 AGGGATAATT
* * *
1036895 TGTTTCAAGAGAAACTGTCTCAAGCGAGAC--AATTTGTTTCAAGGGAAACAATCTCAATTGCTT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTTT
1036958 A
66 A
* * * * **
1036959 TGTTTCAAGAGAAACAGTCTCAAGCGAGACAAAATTTGCTTCAAGGGAAACAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTTT
1037024 A
66 A
* * *
1037025 TGTTTCAAGAGAAAAATGTCTTAAGAGAGACAAAATTTGTTTGAAGGGAAAAAATCTCAATTGTT
1 TGTTTCAAGAG-AAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTT
1037090 TA
65 TA
* * * *
1037092 TGTTTAAAGAGAATCTGTCTTAAGAGAAACAAAACTTTGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAA-TTTGTTTCAAGGGAAAC
1037144 TGTCTCAAGC
Statistics
Matches: 160, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
64 29 0.18
66 61 0.38
67 70 0.44
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTTT
A
Found at i:1049976 original size:25 final size:25
Alignment explanation
Indices: 1049948--1050009 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
1049938 CTTAATGCAT
1049948 ATAATATGAATTCATG-TCATGTATC
1 ATAATATGAATT-ATGATCATGTATC
* *
1049973 ATAATATGAAATGTGATCATGTATC
1 ATAATATGAATTATGATCATGTATC
*
1049998 AAAATATTGAAT
1 ATAATA-TGAAT
1050010 CTAGACTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 25 0.81
26 4 0.13
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (25 bp):
ATAATATGAATTATGATCATGTATC
Found at i:1050332 original size:19 final size:19
Alignment explanation
Indices: 1050308--1050357 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1050298 TTTAAGGGGG
*
1050308 TGCATCGATGTACTCCTTA
1 TGCATCGATGCACTCCTTA
1050327 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
1050346 TGCATCGATGCA
1 TGCATCGATGCA
1050358 TTGATGGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:1050951 original size:13 final size:13
Alignment explanation
Indices: 1050933--1050958 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1050923 GTCTCACGGG
1050933 GAAGAAGAAGAAA
1 GAAGAAGAAGAAA
1050946 GAAGAAGAAGAAA
1 GAAGAAGAAGAAA
1050959 TCTAGAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAA
Done.