Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000046.1 Hibiscus syriacus cultivar Beakdansim tig00000072_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: 55575
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4181 original size:3 final size:3
Alignment explanation
Indices: 4173--4224 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
4163 ACCCATAGCG
4173 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4221 TTA T
1 TTA T
4225 ATCTAAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6119 original size:14 final size:14
Alignment explanation
Indices: 6102--6128 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6092 TTATTTTTTT
6102 TAATTATATTTATA
1 TAATTATATTTATA
6116 TAATTATATTTAT
1 TAATTATATTTAT
6129 TTTTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:6281 original size:22 final size:21
Alignment explanation
Indices: 6253--6293 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
6243 TTATAAAAAT
6253 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
6275 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
6294 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:16460 original size:6 final size:6
Alignment explanation
Indices: 16449--16478 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
16439 CATCGAGCCC
16449 TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT
1 TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT
16479 CTCCTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCCCTT
Found at i:19689 original size:2 final size:2
Alignment explanation
Indices: 19682--19753 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
19672 ATCATAACCC
19682 AT AT 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 AT AT
19724 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
19754 TGTTGGGGAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24493 original size:13 final size:13
Alignment explanation
Indices: 24461--24507 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
24451 ACCGGTCAAC
24461 GGTCAACGGGTCG
1 GGTCAACGGGTCG
24474 GGT---CGGGTCG
1 GGTCAACGGGTCG
24484 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
24497 GGTAAACGGGT
1 GGTCAACGGGT
24508 AAACGGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:24540 original size:10 final size:10
Alignment explanation
Indices: 24520--24563 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
24510 ACGGGTCGTG
24520 ACCGGTC-AA
1 ACCGGTCAAA
24529 ACCGGTCAAA
1 ACCGGTCAAA
*
24539 ACCGGT-TAA
1 ACCGGTCAAA
24548 ACCGGTCAAA
1 ACCGGTCAAA
24558 ACCGGT
1 ACCGGT
24564 TTCCAGCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.34, C:0.30, G:0.23, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:24564 original size:19 final size:19
Alignment explanation
Indices: 24520--24564 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
24510 ACGGGTCGTG
*
24520 ACCGGTCAAACCGGTCAAA
1 ACCGGTTAAACCGGTCAAA
24539 ACCGGTTAAACCGGTCAAA
1 ACCGGTTAAACCGGTCAAA
24558 ACCGGTT
1 ACCGGTT
24565 TCCAGCGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (19 bp):
ACCGGTTAAACCGGTCAAA
Found at i:31740 original size:13 final size:13
Alignment explanation
Indices: 31708--31754 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
31698 ACCGGTCAAC
31708 GGTCAACGGGTCG
1 GGTCAACGGGTCG
31721 GGT---CGGGTCG
1 GGTCAACGGGTCG
31731 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
31744 GGTAAACGGGT
1 GGTCAACGGGT
31755 AAACGGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:31787 original size:10 final size:10
Alignment explanation
Indices: 31767--31810 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
31757 ACGGGTCGTG
31767 ACCGGTC-AA
1 ACCGGTCAAA
31776 ACCGGTCAAA
1 ACCGGTCAAA
*
31786 ACCGGT-TAA
1 ACCGGTCAAA
31795 ACCGGTCAAA
1 ACCGGTCAAA
31805 ACCGGT
1 ACCGGT
31811 TTCCAGCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.34, C:0.30, G:0.23, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:31811 original size:19 final size:19
Alignment explanation
Indices: 31767--31811 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
31757 ACGGGTCGTG
*
31767 ACCGGTCAAACCGGTCAAA
1 ACCGGTTAAACCGGTCAAA
31786 ACCGGTTAAACCGGTCAAA
1 ACCGGTTAAACCGGTCAAA
31805 ACCGGTT
1 ACCGGTT
31812 TCCAGCGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (19 bp):
ACCGGTTAAACCGGTCAAA
Found at i:34550 original size:30 final size:30
Alignment explanation
Indices: 34498--34555 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
34488 TAAAGGTCCT
* * **
34498 CCGATTATAGGGTGATGTTTTGTTGAGTCA
1 CCGACTATAGGATGATACTTTGTTGAGTCA
34528 CCGACTATAGGATGATACTTTGTTGAGT
1 CCGACTATAGGATGATACTTTGTTGAGT
34556 ATATCGACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (30 bp):
CCGACTATAGGATGATACTTTGTTGAGTCA
Found at i:35370 original size:15 final size:16
Alignment explanation
Indices: 35332--35372 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
35322 ACAGAGCATC
* *
35332 TGAATCATTCATCATT
1 TGAATCATTCAGCACT
35348 TGAATCATTCAGCACT
1 TGAATCATTCAGCACT
35364 T-AATCATTC
1 TGAATCATTC
35373 TGAAATAAAC
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:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:35502 original size:17 final size:17
Alignment explanation
Indices: 35449--35506 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
35439 TATTTGTATC
*
35449 ATTA-TTAAAATTATTT
1 ATTATTTAAAATTTTTT
*
35465 ATAATTTAAAATATTTGTT
1 ATTATTTAAAAT-TTT-TT
*
35484 ATTATTTCAAATTTTTT
1 ATTATTTAAAATTTTTT
35501 ATTATT
1 ATTATT
35507 ATTTATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.09
17 15 0.43
18 5 0.14
19 12 0.34
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTATTTAAAATTTTTT
Found at i:40650 original size:15 final size:16
Alignment explanation
Indices: 40630--40660 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
40620 GTGTGCATGC
40630 GTATGATCATG-TCCA
1 GTATGATCATGATCCA
40645 GTATGATCATGATCCA
1 GTATGATCATGATCCA
40661 CGAAGTCAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (16 bp):
GTATGATCATGATCCA
Found at i:41454 original size:11 final size:11
Alignment explanation
Indices: 41438--41465 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
41428 TGTAAAAGAT
41438 GTAAATGCAAA
1 GTAAATGCAAA
41449 GTAAATGCAAA
1 GTAAATGCAAA
41460 GTAAAT
1 GTAAAT
41466 CTCTCACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (11 bp):
GTAAATGCAAA
Found at i:51459 original size:30 final size:30
Alignment explanation
Indices: 51377--51448 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
51367 CTCCTACTAA
** * *
51377 GAACAAAATTGAAGTTATTGCTGCTGTCTC
1 GAACAAAGCTGAAGTTATTGCTGATGTCAC
*
51407 GAACAAAGCTGAAGTTACTGCTGATGTCAC
1 GAACAAAGCTGAAGTTATTGCTGATGTCAC
*
51437 GATCAAAGCTGA
1 GAACAAAGCTGA
51449 TATTGTTGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (30 bp):
GAACAAAGCTGAAGTTATTGCTGATGTCAC
Done.