Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008143.1 Hibiscus syriacus cultivar Beakdansim tig00110705_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: 1142845
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1104646 original size:41 final size:41
Alignment explanation
Indices: 1104327--1104630 Score: 520
Period size: 41 Copynumber: 7.4 Consensus size: 41
1104317 AACTTCGACT
* *
1104327 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGG-CTATCGCAATGCGAATATGTAA
*
1104368 ATCGCAATGCGATAGTCGGCTATCGCAATACGAATATGTAA
1 ATCGCAATGCGATAGTCGGCTATCGCAATGCGAATATGTAA
*
1104409 ATCGCAATGCGATAGTCCGCTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGGCTATCGCAATGCGAATATGTAA
*
1104450 ATCGCAATACGATAGTCGGCTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGGCTATCGCAATGCGAATATGTAA
*
1104491 ATCGCAATGCGATAGTTGGCTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGGCTATCGCAATGCGAATATGTAA
* *
1104532 ATCGCAATACGATAGTCGGCTATCGCAATCCGAATATGTAA
1 ATCGCAATGCGATAGTCGGCTATCGCAATGCGAATATGTAA
1104573 ATCGCAATGCGATAGTCGGCTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGGCTATCGCAATGCGAATATGTAA
1104614 ATCGCAATGCGATAGTC
1 ATCGCAATGCGATAGTC
1104631 CAAGTTCGCG
Statistics
Matches: 248, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
41 244 0.98
42 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (41 bp):
ATCGCAATGCGATAGTCGGCTATCGCAATGCGAATATGTAA
Found at i:1104772 original size:6 final size:6
Alignment explanation
Indices: 1104761--1104820 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
1104751 GACACGTATT
*
1104761 ACCACG ACCACG ACCACG ACGACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1104808 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
1104821 CGAGACGGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
5 15 0.29
6 37 0.71
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1104811 original size:5 final size:5
Alignment explanation
Indices: 1104783--1104823 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
1104773 ACCACGACGA
1104783 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
1104824 GACGGACGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:1105392 original size:21 final size:21
Alignment explanation
Indices: 1105366--1105433 Score: 90
Period size: 20 Copynumber: 3.3 Consensus size: 21
1105356 CCACCAGTCG
1105366 TTGCGATTTTGGAC-TA-TCGCA
1 TTGCGATTTT--ACATATTCGCA
1105387 TTGCGA-TTTACATATTCGCA
1 TTGCGATTTTACATATTCGCA
1105407 TTGCGA-TTTACATATTCGCA
1 TTGCGATTTTACATATTCGCA
1105427 TTGCGAT
1 TTGCGAT
1105434 AGTCGAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 34 0.77
21 6 0.14
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
TTGCGATTTTACATATTCGCA
Found at i:1105407 original size:20 final size:20
Alignment explanation
Indices: 1105382--1105433 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1105372 TTTTGGACTA
1105382 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1105402 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1105422 TCGCATTGCGAT
1 TCGCATTGCGAT
1105434 AGTCGAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1107810 original size:8 final size:8
Alignment explanation
Indices: 1107797--1107844 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1107787 TTAGTGTTAG
1107797 GATTTTGA
1 GATTTTGA
*
1107805 GATTTTAGG
1 GATTTT-GA
1107814 GATTTTGA
1 GATTTTGA
*
1107822 GATTTTAGG
1 GATTTT-GA
1107831 GATTTTGA
1 GATTTTGA
*
1107839 GGTTTT
1 GATTTT
1107845 TTTATAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
8 19 0.58
9 14 0.42
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (8 bp):
GATTTTGA
Found at i:1107818 original size:17 final size:17
Alignment explanation
Indices: 1107796--1107844 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
1107786 GTTAGTGTTA
1107796 GGATTTTGAGATTTTAG
1 GGATTTTGAGATTTTAG
1107813 GGATTTTGAGATTTTAG
1 GGATTTTGAGATTTTAG
*
1107830 GGATTTTGAGGTTTT
1 GGATTTTGAGATTTT
1107845 TTTATAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (17 bp):
GGATTTTGAGATTTTAG
Found at i:1112906 original size:18 final size:18
Alignment explanation
Indices: 1112868--1112907 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1112858 GCCCTCCATT
*
1112868 TTCTTTGCCACCTTTTGA
1 TTCTTTGCCACCCTTTGA
1112886 TTCTTTGCC-CCCTTTGAA
1 TTCTTTGCCACCCTTTG-A
1112904 TTCT
1 TTCT
1112908 CCTCCTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.10, C:0.30, G:0.10, T:0.50
Consensus pattern (18 bp):
TTCTTTGCCACCCTTTGA
Found at i:1113112 original size:60 final size:60
Alignment explanation
Indices: 1113017--1113203 Score: 207
Period size: 60 Copynumber: 3.1 Consensus size: 60
1113007 CCCCCACCAG
* * * *
1113017 GCCCACCCGGAACTCCGAATCCACC-CGAGACAGTTCCAAACCCACCTAGCATTTTTCCAA
1 GCCCACCCGGAACTCCAAATCCACCAC-AAATAGTTCCAAACCCACCTAGTATTTTTCCAA
* * * * * **
1113077 GCCCACCTGGAGCTCTAAATCCACCTGC-AATAGTTCCAAGCCCACCTAGTACCTTTCCAA
1 GCCCACCCGGAACTCCAAATCCACC-ACAAATAGTTCCAAACCCACCTAGTATTTTTCCAA
* * * *
1113137 ACCCGCCCGGAACTCCAAATCCACCACAAATAGTTCCAAACCCACCTAGTGTTTTCCCAA
1 GCCCACCCGGAACTCCAAATCCACCACAAATAGTTCCAAACCCACCTAGTATTTTTCCAA
1113197 GCCCACC
1 GCCCACC
1113204 ACATGCGATA
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
59 1 0.01
60 99 0.98
62 1 0.01
ACGTcount: A:0.28, C:0.41, G:0.12, T:0.18
Consensus pattern (60 bp):
GCCCACCCGGAACTCCAAATCCACCACAAATAGTTCCAAACCCACCTAGTATTTTTCCAA
Found at i:1116208 original size:5 final size:5
Alignment explanation
Indices: 1116190--1116244 Score: 87
Period size: 5 Copynumber: 11.4 Consensus size: 5
1116180 CCGCCGCCGC
1116190 CGTC- CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
*
1116238 CGGCT CG
1 CGTCT CG
1116245 GGTCGGGTCG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
4 8 0.16
5 41 0.84
ACGTcount: A:0.00, C:0.42, G:0.24, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:1116286 original size:6 final size:6
Alignment explanation
Indices: 1116245--1116361 Score: 149
Period size: 6 Copynumber: 20.5 Consensus size: 6
1116235 TCTCGGCTCG
1116245 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
**
1116287 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTAAT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
*
1116335 ACGT-GT GGTCGT GGTCGT GGTCGT GGT
1 -GGTCGT GGTCGT GGTCGT GGTCGT GGT
1116362 AATACGTGTC
Statistics
Matches: 104, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
5 32 0.31
6 70 0.67
7 2 0.02
ACGTcount: A:0.03, C:0.16, G:0.51, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:1121803 original size:36 final size:37
Alignment explanation
Indices: 1121731--1121803 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
1121721 GTTGGAAAAT
* *
1121731 ATTTATATATATTTTTTTAAAAATTTAAATTCATAAA
1 ATTTATATATATTTTTTTAAAAATTGAAAATCATAAA
1121768 ATTTATATA-ATTTTTTTATAAAATTGAAAAT-ATAAA
1 ATTTATATATATTTTTTTA-AAAATTGAAAATCATAAA
1121804 CAGGTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 14 0.42
37 19 0.58
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTATATATATTTTTTTAAAAATTGAAAATCATAAA
Found at i:1133541 original size:28 final size:29
Alignment explanation
Indices: 1133474--1133553 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 29
1133464 CCCCCCCTAC
* *
1133474 ATTTAGGTTAATGAATTTAAATATTTATT
1 ATTTAGGTTAATAAATTTAAATATTTAAT
** *
1133503 ATTTATTTTAA-AACATTTTAA-ATTTAAT
1 ATTTAGGTTAATAA-ATTTAAATATTTAAT
* *
1133531 ATTTAGGTTAATCAATTAAAATA
1 ATTTAGGTTAATAAATTTAAATA
1133554 CTAACATTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (29 bp):
ATTTAGGTTAATAAATTTAAATATTTAAT
Found at i:1134724 original size:13 final size:13
Alignment explanation
Indices: 1134706--1134730 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1134696 TTTGATTTGC
1134706 GAGTTTTCCATTT
1 GAGTTTTCCATTT
1134719 GAGTTTTCCATT
1 GAGTTTTCCATT
1134731 GGAAGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (13 bp):
GAGTTTTCCATTT
Found at i:1141297 original size:24 final size:24
Alignment explanation
Indices: 1141253--1141299 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1141243 ATAAAGAACC
*
1141253 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1141277 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
1141300 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Done.