Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002876.1 Hibiscus syriacus cultivar Beakdansim tig00005930_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: 50648
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:1080 original size:19 final size:20
Alignment explanation
Indices: 1039--1082 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1029 TTTTTAAAAC
1039 TTTTA-AATTTTTTACATGA
1 TTTTATAATTTTTTACATGA
*
1058 -TTTATAATTTTTTATAT-A
1 TTTTATAATTTTTTACATGA
1076 TTTTATA
1 TTTTATA
1083 TTAATAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTATAATTTTTTACATGA
Found at i:3989 original size:13 final size:13
Alignment explanation
Indices: 3957--3994 Score: 69
Period size: 12 Copynumber: 3.0 Consensus size: 13
3947 GCAGCTCTTC
3957 CTTAAATTGTTCT
1 CTTAAATTGTTCT
3970 CTT-AATTGTTCT
1 CTTAAATTGTTCT
3982 CTTAAATTGTTCT
1 CTTAAATTGTTCT
3995 TGGTTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (13 bp):
CTTAAATTGTTCT
Found at i:5225 original size:2 final size:2
Alignment explanation
Indices: 5218--5255 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5208 TGATTACAAA
5218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5256 TTTTTAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6108 original size:16 final size:16
Alignment explanation
Indices: 6090--6244 Score: 247
Period size: 16 Copynumber: 9.7 Consensus size: 16
6080 TAGTTGGACT
*
6090 GAAAGCAACCCGAACT
1 GAAAGCAACCCGAACC
* *
6106 GAAAGAAACTCGAACC
1 GAAAGCAACCCGAACC
6122 GAAAGCAACCCGAACC
1 GAAAGCAACCCGAACC
* *
6138 GAAAGTAACTCGAACC
1 GAAAGCAACCCGAACC
6154 GAAAGCAACCCGAACC
1 GAAAGCAACCCGAACC
* *
6170 GAAAGCAACTCGAACT
1 GAAAGCAACCCGAACC
6186 GAAAGCAACCCGAACC
1 GAAAGCAACCCGAACC
6202 GAAAGCAACCCGAACC
1 GAAAGCAACCCGAACC
6218 GAAAGCAACCCGAACC
1 GAAAGCAACCCGAACC
6234 GAAAGCAACCC
1 GAAAGCAACCC
6245 AAATTTAGTT
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 126 1.00
ACGTcount: A:0.45, C:0.33, G:0.19, T:0.04
Consensus pattern (16 bp):
GAAAGCAACCCGAACC
Found at i:6733 original size:20 final size:20
Alignment explanation
Indices: 6710--6771 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
6700 GATTGGCCTA
*
6710 AAAATATAAAGATTTGCCCG
1 AAAATATAAAGATTAGCCCG
* * *
6730 AAAATATTAAGGTTAACCCG
1 AAAATATAAAGATTAGCCCG
* * *
6750 AAAATCTAAAGACTGGCCCG
1 AAAATATAAAGATTAGCCCG
6770 AA
1 AA
6772 TTGAAAAATA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (20 bp):
AAAATATAAAGATTAGCCCG
Found at i:7230 original size:18 final size:18
Alignment explanation
Indices: 7207--7256 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
7197 TTTTTGTTTG
7207 GTTGTTCATATTCTTCTA
1 GTTGTTCATATTCTTCTA
7225 GTTGTTCATATTCTTCTA
1 GTTGTTCATATTCTTCTA
*
7243 GTTGTTCATTTTCT
1 GTTGTTCATATTCT
7257 ATGGATTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.58
Consensus pattern (18 bp):
GTTGTTCATATTCTTCTA
Found at i:9052 original size:12 final size:12
Alignment explanation
Indices: 9035--9060 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9025 CATTACTGAT
9035 GTATTATATCAA
1 GTATTATATCAA
9047 GTATTATATCAA
1 GTATTATATCAA
9059 GT
1 GT
9061 TTTGCAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (12 bp):
GTATTATATCAA
Found at i:9207 original size:15 final size:15
Alignment explanation
Indices: 9187--9226 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
9177 GTGAAAAGAA
9187 TGAATTAAATGTTCT
1 TGAATTAAATGTTCT
9202 TGAATTAAATGTTCT
1 TGAATTAAATGTTCT
9217 TGAATTAAAT
1 TGAATTAAAT
9227 ATACAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (15 bp):
TGAATTAAATGTTCT
Found at i:16294 original size:21 final size:21
Alignment explanation
Indices: 16268--16309 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16258 GAGTCGAGGG
16268 TCTACGCGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
*
16289 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
16310 AATTCTACGC
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:0.14, C:0.31, G:0.29, T:0.26
Consensus pattern (21 bp):
TCTACGCGGTCCTTCGGGACA
Found at i:17324 original size:59 final size:59
Alignment explanation
Indices: 17134--17715 Score: 863
Period size: 59 Copynumber: 10.0 Consensus size: 59
17124 GGGGCGTTAC
* * * * *
17134 AGTGCCCTATCTAGAAATTCATACGCTTAGTATGATTTTCTTATCTTTTTAGCACACTTA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACAC-GA
* * *
17194 A-TGCCCTATCTAGAAA-TCATTCACTTAGTATGATTTTCTTATCG--TT---ACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
17246 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* * *
17305 AGTACCCTATATGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACTA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* *
17364 AGTGCCCTATCTGGAAATTCATATACTTAGTATGATTTTCTTATCGTTTTAGCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* * * *
17423 AGTACCCTATCTTGAAATTCATACACTTAATATGATTTCCTTATCGTTTTAGAACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* *
17482 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCTTTATCGTTTTATCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* *
17541 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTTCTTATCGTTTCAGCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* * **
17600 ATTGCCCTATCCGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTTTCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* *
17659 AGTGCCCTATCTGGAAATTCATACATTTAGTATGATTTCCTTATCATTTTAGCACAC
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACAC
17716 TTAGTGACCT
Statistics
Matches: 472, Mismatches: 43, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
52 2 0.00
53 18 0.04
54 26 0.06
56 4 0.01
58 25 0.05
59 396 0.84
60 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (59 bp):
AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
Found at i:18188 original size:22 final size:23
Alignment explanation
Indices: 18150--18213 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
18140 CTGGCGTCGA
18150 TACCCTTACCATGGTATCGATAC
1 TACCCTTACCATGGTATCGATAC
*
18173 TACCCTT-CTATGGTATCGATAC
1 TACCCTTACCATGGTATCGATAC
*
18195 --CCCCTACCA--GTATCGATAC
1 TACCCTTACCATGGTATCGATAC
18214 CAAAATTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.27
20 4 0.11
21 2 0.05
22 14 0.38
23 7 0.19
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (23 bp):
TACCCTTACCATGGTATCGATAC
Found at i:18308 original size:96 final size:95
Alignment explanation
Indices: 18109--18288 Score: 240
Period size: 95 Copynumber: 1.9 Consensus size: 95
18099 CCCCATTTGG
* * * *
18109 GTATCGATACCAAAAATAGGTTTGATGTTTCCTGGCGTCGATACCCTTACCATGGTATCGATACT
1 GTATCGATACCAAAAATAGATTCGATGTTTCATGGCATCGATACCCTTACCATGGTATCGATACT
* *
18174 ACCCTTCTATGGTATCGATACCCCCTACCA
66 ACCCTTCTATGATATCGATACCCACTACCA
* * *
18204 GTATCGATACCAAAATTAGATTCGATGTTTCATGGTATCGATACCCCTTATCATGGTATCGATAC
1 GTATCGATACCAAAAATAGATTCGATGTTTCATGGCATCGATA-CCCTTACCATGGTATCGATAC
18269 TA-CC-TCT-TAGATATCGATAC
65 TACCCTTCTAT-GATATCGATAC
18289 TGATTGAATC
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
93 1 0.01
94 13 0.17
95 39 0.52
96 22 0.29
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (95 bp):
GTATCGATACCAAAAATAGATTCGATGTTTCATGGCATCGATACCCTTACCATGGTATCGATACT
ACCCTTCTATGATATCGATACCCACTACCA
Found at i:19594 original size:2 final size:2
Alignment explanation
Indices: 19577--19618 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
19567 AAAGTTTCAA
19577 AT AT AGT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19619 GAAGTGTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20899 original size:21 final size:21
Alignment explanation
Indices: 20874--20917 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
20864 GAAAATGTTA
* *
20874 AAAAATATTAATGTTTTAAAT
1 AAAAATAATAATATTTTAAAT
20895 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
20916 AA
1 AA
20918 TTTTTTACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:25589 original size:18 final size:18
Alignment explanation
Indices: 25566--25607 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
25556 CAAAACAAGT
25566 TACAGACTCCGATATACA
1 TACAGACTCCGATATACA
25584 TACAGACTCCGATATACA
1 TACAGACTCCGATATACA
25602 TACAGA
1 TACAGA
25608 ATGAGACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.21
Consensus pattern (18 bp):
TACAGACTCCGATATACA
Found at i:28089 original size:4 final size:4
Alignment explanation
Indices: 28080--28110 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
28070 CAATGCATGT
*
28080 ATAA ATAA ATAA ATAA ATGA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
28111 CATAGTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Done.