Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003709.1 Hibiscus syriacus cultivar Beakdansim tig00007935_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: 61070
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:7234 original size:20 final size:22
Alignment explanation
Indices: 7195--7234 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
7185 GGCTTTAGCT
*
7195 AAGCATAATGCATTGATTGTCG
1 AAGCATAATGCATAGATTGTCG
7217 AAGCAT-ATGC-TAGATTGT
1 AAGCATAATGCATAGATTGT
7235 TAATAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (22 bp):
AAGCATAATGCATAGATTGTCG
Found at i:17353 original size:2 final size:2
Alignment explanation
Indices: 17348--17377 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17338 ACACACACAC
17348 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
17378 TTTAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17413 original size:26 final size:26
Alignment explanation
Indices: 17383--17433 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
17373 TATATTTTAA
17383 TTTATCAATAAA-TAATTATTTATTAC
1 TTTATCAATAAATTAA-TATTTATTAC
**
17409 TTTATTGATAAATTAATATTTATTA
1 TTTATCAATAAATTAATATTTATTA
17434 ATAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTATCAATAAATTAATATTTATTAC
Found at i:19945 original size:20 final size:21
Alignment explanation
Indices: 19920--19958 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19910 GGCTGCTGGA
19920 AATCGGTT-TAACCGGTTTTC
1 AATCGGTTCTAACCGGTTTTC
*
19940 AATCGGTTCTGACCGGTTT
1 AATCGGTTCTAACCGGTTT
19959 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (21 bp):
AATCGGTTCTAACCGGTTTTC
Found at i:19995 original size:49 final size:50
Alignment explanation
Indices: 19929--20033 Score: 135
Period size: 49 Copynumber: 2.1 Consensus size: 50
19919 AAATCGGTTT
* *
19929 AACCGGTTTTCAATCGGTTCT-GACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTTCAATCGG-TCTAAACCGGTTTGACCGGTCTCAACCGGTTCG
* * *
19979 AACCGGTTTT-GATCGGTCTAAACCGGTTTGACCGGTCTGAACCGGTTTG
1 AACCGGTTTTCAATCGGTCTAAACCGGTTTGACCGGTCTCAACCGGTTCG
20028 -ACCGGT
1 AACCGGT
20034 CTGACCCGAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 9 0.18
49 30 0.61
50 10 0.20
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (50 bp):
AACCGGTTTTCAATCGGTCTAAACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:20034 original size:19 final size:19
Alignment explanation
Indices: 19943--20037 Score: 104
Period size: 19 Copynumber: 4.9 Consensus size: 19
19933 GGTTTTCAAT
*
19943 CGGTTCTGACCGGTTTG-AC
1 CGGTT-TGACCGGTCTGAAC
*
19962 CGGTTTCAACCGGT-TCGAAC
1 CGGTTT-GACCGGTCT-GAAC
* *
19982 CGGTTTTGATCGGTCTAAAC
1 CGG-TTTGACCGGTCTGAAC
20002 CGGTTTGACCGGTCTGAAC
1 CGGTTTGACCGGTCTGAAC
20021 CGGTTTGACCGGTCTGA
1 CGGTTTGACCGGTCTGA
20038 CCCGACCCGA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
18 2 0.03
19 43 0.66
20 16 0.25
21 4 0.06
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.29
Consensus pattern (19 bp):
CGGTTTGACCGGTCTGAAC
Found at i:20038 original size:9 final size:9
Alignment explanation
Indices: 20000--20039 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
19990 ATCGGTCTAA
*
20000 ACCGGTTTG
1 ACCGGTCTG
20009 ACCGGTCTG
1 ACCGGTCTG
*
20018 AACCGGTTTG
1 -ACCGGTCTG
20028 ACCGGTCTG
1 ACCGGTCTG
20037 ACC
1 ACC
20040 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:20057 original size:17 final size:17
Alignment explanation
Indices: 20035--20090 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
20025 TTGACCGGTC
20035 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
20052 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
20069 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
20086 TGACC
1 TGACC
20091 GTTGACTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:26594 original size:20 final size:21
Alignment explanation
Indices: 26569--26607 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26559 GGCTGCTGGA
26569 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
26589 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
26608 GACCAGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:26650 original size:20 final size:19
Alignment explanation
Indices: 26569--26667 Score: 76
Period size: 20 Copynumber: 5.1 Consensus size: 19
26559 GGCTGCTGGA
* * *
26569 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
*
26589 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
* *
26609 -ACCAGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
*
26628 AACCGGTTTTGACCTGTCTG
1 AACCGG-TTTGACCGGTCTG
26648 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
26667 A
1 A
26668 CCCGACCCGA
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.03
19 26 0.40
20 27 0.42
21 10 0.15
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:26659 original size:19 final size:20
Alignment explanation
Indices: 26589--26667 Score: 74
Period size: 19 Copynumber: 4.0 Consensus size: 20
26579 ACCGGTTTTC
* *
26589 AACCGGTTCTGACCGGTTTG
1 AACCGGTTTTGACCGGTCTG
* **
26609 -ACCAGTTTCAACCGGT-TCG
1 AACCGGTTTTGACCGGTCT-G
*
26628 AACCGGTTTTGACCTGTCTG
1 AACCGGTTTTGACCGGTCTG
26648 AACCGG-TTTGACCGGTCTG
1 AACCGGTTTTGACCGGTCTG
26667 A
1 A
26668 CCCGACCCGA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.02
19 26 0.55
20 19 0.40
21 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (20 bp):
AACCGGTTTTGACCGGTCTG
Found at i:26663 original size:9 final size:9
Alignment explanation
Indices: 26570--26669 Score: 65
Period size: 10 Copynumber: 10.3 Consensus size: 9
26560 GCTGCTGGAA
*
26570 ACCGGTTTA
1 ACCGGTTTG
*
26579 ACCGGTTTTCA
1 ACCGG-TTT-G
26590 ACCGGTTCTG
1 ACCGGTT-TG
26600 ACCGGTTTG
1 ACCGGTTTG
* *
26609 ACCAGTTTCA
1 ACCGGTTT-G
*
26619 ACCGGTTCG
1 ACCGGTTTG
26628 AACCGGTTTTG
1 -ACCGG-TTTG
* *
26639 ACCTGTCTG
1 ACCGGTTTG
26648 AACCGGTTTG
1 -ACCGGTTTG
*
26658 ACCGGTCTG
1 ACCGGTTTG
26667 ACC
1 ACC
26670 CGACCCGACC
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
9 28 0.39
10 34 0.47
11 10 0.14
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:26676 original size:5 final size:5
Alignment explanation
Indices: 26666--26718 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
26656 TGACCGGTCT
* *
26666 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
26715 GACC
1 GACC
26719 GCTGACCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:26687 original size:17 final size:17
Alignment explanation
Indices: 26665--26725 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
26655 TTGACCGGTC
26665 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
26682 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
*
26704 TGACCCGACCCGACCGC
1 TGACCCGACCCGACCGT
26721 TGACC
1 TGACC
26726 GTTGACTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 21 0.55
22 17 0.45
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:26692 original size:22 final size:22
Alignment explanation
Indices: 26666--26731 Score: 114
Period size: 22 Copynumber: 2.9 Consensus size: 22
26656 TGACCGGTCT
26666 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
26688 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
26710 GACCCGACCGCTGACCGTTGAC
1 GACCCGACC-C-GACCGTTGAC
26732 TTTCTTTGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 31 0.74
23 1 0.02
24 10 0.24
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:41308 original size:6 final size:6
Alignment explanation
Indices: 41299--41344 Score: 57
Period size: 5 Copynumber: 8.5 Consensus size: 6
41289 CATTACCATT
41299 ACCACG ACCACG ACCACG A-CACG A-CACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
41342 ACC
1 ACC
41345 CGAGACGGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 25 0.64
6 14 0.36
ACGTcount: A:0.30, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:41848 original size:6 final size:6
Alignment explanation
Indices: 41837--41863 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41827 TCTCGTCTCG
41837 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
41864 AATACGCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:41924 original size:41 final size:41
Alignment explanation
Indices: 41867--42040 Score: 242
Period size: 41 Copynumber: 4.2 Consensus size: 41
41857 TCGTGGTAAT
* *
41867 ACGCGAAATGGAAAATCGCAACGCGACTGT-AGACTATCGCA
1 ACGCGAAATGGAAAATCGCAACGCGATTTTCA-ACTATCGCA
***
41908 ACGCGAAATGGAAAATCGCGTTGCGATTTTCAACTATCGCA
1 ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
* ***
41949 ACGCGAAATAGAAAATCGCGTTGCGATTTTCAACTATCGCA
1 ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
*
41990 ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATTGCA
1 ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
42031 ACGCGAAATG
1 ACGCGAAATG
42041 CAACTCGAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
41 120 0.99
42 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (41 bp):
ACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
Found at i:41995 original size:21 final size:21
Alignment explanation
Indices: 41930--42036 Score: 74
Period size: 21 Copynumber: 5.2 Consensus size: 21
41920 AAATCGCGTT
41930 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** * ***
41951 GCGAAATAGAA-AATCGCGTT
1 GCGATTTTCAACTATCGCAAC
41971 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** *
41992 GCGAAATGGAA-AATCGCAAC
1 GCGATTTTCAACTATCGCAAC
*
42012 GCGATTTTCAACTATTGCAAC
1 GCGATTTTCAACTATCGCAAC
42033 GCGA
1 GCGA
42037 AATGCAACTC
Statistics
Matches: 57, Mismatches: 27, Indels: 4
0.65 0.31 0.05
Matches are distributed among these distances:
20 27 0.47
21 30 0.53
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:42044 original size:21 final size:21
Alignment explanation
Indices: 41867--42045 Score: 73
Period size: 21 Copynumber: 8.7 Consensus size: 21
41857 TCGTGGTAAT
* *
41867 ACGCGAAATGGAA-AATCGCA
1 ACGCGAAATGCAACTATCGCA
* *
41887 ACGCG-ACTGTAGACTATCGCA
1 ACGCGAAATGCA-ACTATCGCA
* * *
41908 ACGCGAAATGGAA-AATCGCG
1 ACGCGAAATGCAACTATCGCA
** ** *
41928 TTGCGATTTTCAACTATCGCA
1 ACGCGAAATGCAACTATCGCA
* *
41949 ACGCGAAATAG-AA-AATCGCG
1 ACGCGAAAT-GCAACTATCGCA
** ** *
41969 TTGCGATTTTCAACTATCGCA
1 ACGCGAAATGCAACTATCGCA
* *
41990 ACGCGAAATGGAA-AATCGCA
1 ACGCGAAATGCAACTATCGCA
** * *
42010 ACGCGATTTTCAACTATTGCA
1 ACGCGAAATGCAACTATCGCA
42031 ACGCGAAATGCAACT
1 ACGCGAAATGCAACT
42046 CGAATTTGCG
Statistics
Matches: 106, Mismatches: 45, Indels: 15
0.64 0.27 0.09
Matches are distributed among these distances:
19 4 0.04
20 45 0.42
21 53 0.50
22 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
ACGCGAAATGCAACTATCGCA
Found at i:42057 original size:41 final size:41
Alignment explanation
Indices: 41899--42057 Score: 196
Period size: 41 Copynumber: 3.9 Consensus size: 41
41889 GCGACTGTAG
* **
41899 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATAGAAAATCGAATTGCGATTTTCA
**
41940 ACTATCGCAACGCGAAATAGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATAGAAAATCGAATTGCGATTTTCA
* *
41981 ACTATCGCAACGCGAAATGGAAAATCGCAA-CGCGATTTTCA
1 ACTATCGCAACGCGAAATAGAAAATCG-AATTGCGATTTTCA
* * *
42022 ACTATTGCAACGCGAAAT-GCAACTCGAATTTGCGAT
1 ACTATCGCAACGCGAAATAGAAAATCGAA-TTGCGAT
42058 AGTGGAGATC
Statistics
Matches: 106, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.02
40 6 0.06
41 98 0.92
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATAGAAAATCGAATTGCGATTTTCA
Found at i:42190 original size:3 final size:3
Alignment explanation
Indices: 42182--42239 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
42172 TTATTTTCTC
* ** *
42182 TTA TTA TTA TTA TTA TTA TGA TTA TTA AAA TTA TTA TTT TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
42231 TTA TTA TTA
1 TTA TTA TTA
42240 AAATAATAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:50628 original size:15 final size:15
Alignment explanation
Indices: 50592--50628 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
50582 ATACCATAAT
*
50592 GATCGAGTTCTCCGC
1 GATCGATTTCTCCGC
50607 GATCGATTTCTCCGC
1 GATCGATTTCTCCGC
50622 GATCGAT
1 GATCGAT
50629 GCCAATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.30
Consensus pattern (15 bp):
GATCGATTTCTCCGC
Done.