Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007253.1 Hibiscus syriacus cultivar Beakdansim tig00019216_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: 70431
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:727 original size:21 final size:21
Alignment explanation
Indices: 680--728 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
670 CCGATCATCC
* *
680 AATTTTTTAAACCTCAGACCG
1 AATTTTTTAAACCCCAGACCA
* *
701 GA-TTTTTAAACCCCATACCA
1 AATTTTTTAAACCCCAGACCA
721 AATTTTTT
1 AATTTTTT
729 TCCGGATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (21 bp):
AATTTTTTAAACCCCAGACCA
Found at i:866 original size:19 final size:20
Alignment explanation
Indices: 827--867 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
817 CGGTTATACT
*
827 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTAAAAATATCCG
847 ATCCGGTTTAAAAATA-CCG
1 ATCCGGTTTAAAAATATCCG
866 AT
1 AT
868 TTTTCCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (20 bp):
ATCCGGTTTAAAAATATCCG
Found at i:4860 original size:20 final size:20
Alignment explanation
Indices: 4832--4872 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4822 TGAATTTTCA
*
4832 AAATTTATTTTTGAAA-TTAT
1 AAATATATTTTT-AAACTTAT
4852 AAATATATTTTTAAACTTAT
1 AAATATATTTTTAAACTTAT
4872 A
1 A
4873 TTTAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATATATTTTTAAACTTAT
Found at i:6140 original size:47 final size:48
Alignment explanation
Indices: 6086--6176 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
6076 GTATTTTAAT
* *
6086 GTGAATTTAG-AATTTATATTGAAAATTTAAGAGCATAAACTTACAAA
1 GTGAATTTAGAAAATTATACTGAAAATTTAAGAGCATAAACTTACAAA
* **
6133 GTGAATTTAGAAAATTATACTGAAAATTTAGGAGTGTAAACTTA
1 GTGAATTTAGAAAATTATACTGAAAATTTAAGAGCATAAACTTA
6177 TAAAATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 10 0.26
48 28 0.74
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.34
Consensus pattern (48 bp):
GTGAATTTAGAAAATTATACTGAAAATTTAAGAGCATAAACTTACAAA
Found at i:28421 original size:17 final size:17
Alignment explanation
Indices: 28395--28428 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28385 GAGGGATAAG
28395 TTTTAATAAAATATATT
1 TTTTAATAAAATATATT
* *
28412 TTTTATTAAAATTTATT
1 TTTTAATAAAATATATT
28429 AGTTTGATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAATAAAATATATT
Found at i:31517 original size:2 final size:2
Alignment explanation
Indices: 31510--31558 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
31500 TATTTTACTC
31510 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
31552 AT AT AT A
1 AT AT AT A
31559 CACACTGTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33095 original size:4 final size:4
Alignment explanation
Indices: 33078--33114 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
33068 TTCCCCAATG
*
33078 TACA TACA TTCA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
33115 TTGCTTCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (4 bp):
TACA
Found at i:44538 original size:9 final size:9
Alignment explanation
Indices: 44524--44592 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
44514 GTGGCTGAAA
44524 ACCGGTTTG
1 ACCGGTTTG
44533 ACCGGTTTTG
1 ACCGG-TTTG
44543 ACCGGTTTG
1 ACCGGTTTG
* *
44552 ATCGATTTCG
1 ACCGGTTT-G
**
44562 ACCGGTTCAA
1 ACCGGTT-TG
44572 ACCGGTTTG
1 ACCGGTTTG
* *
44581 CCCGGTCTG
1 ACCGGTTTG
44590 ACC
1 ACC
44593 CGACCCGACC
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 24 0.52
10 22 0.48
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:44548 original size:19 final size:19
Alignment explanation
Indices: 44524--44568 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
44514 GTGGCTGAAA
* *
44524 ACCGGTTTGACCGGTTTTG
1 ACCGGTTTGACCGATTTCG
*
44543 ACCGGTTTGATCGATTTCG
1 ACCGGTTTGACCGATTTCG
44562 ACCGGTT
1 ACCGGTT
44569 CAAACCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.29, T:0.36
Consensus pattern (19 bp):
ACCGGTTTGACCGATTTCG
Found at i:44616 original size:17 final size:17
Alignment explanation
Indices: 44594--44629 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
44584 GGTCTGACCC
44594 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
44611 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
44628 GA
1 GA
44630 TCGTGACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.44, G:0.25, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:49169 original size:10 final size:10
Alignment explanation
Indices: 49141--49177 Score: 58
Period size: 11 Copynumber: 3.7 Consensus size: 10
49131 TGAAAATCGG
49141 TTTGACCGGT
1 TTTGACCGGT
49151 TTTGAACCGGT
1 TTTG-ACCGGT
49162 TTTGACCGG-
1 TTTGACCGGT
49171 TTTGACC
1 TTTGACC
49178 AATTTCAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 7 0.27
10 9 0.35
11 10 0.38
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (10 bp):
TTTGACCGGT
Found at i:49256 original size:17 final size:17
Alignment explanation
Indices: 49226--49261 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
49216 CAACCCGACC
49226 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
* *
49243 GACCCTACCTGACCGTT
1 GACCCGACCCGACCGTT
49260 GA
1 GA
49262 TCGTGACTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.42, G:0.22, T:0.17
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:51965 original size:17 final size:16
Alignment explanation
Indices: 51928--51966 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
51918 TTTAAATTTT
*
51928 AATTTAAAACATTATA
1 AATTTAAAACATTAAA
*
51944 TATTTAAATACATTAAA
1 AATTTAAA-ACATTAAA
51961 AATTTA
1 AATTTA
51967 TCACTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAAACATTAAA
Found at i:66617 original size:15 final size:17
Alignment explanation
Indices: 66583--66620 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
66573 AAAAAGATAA
*
66583 TAAAAATATAATTATAT
1 TAAAAAGATAATTATAT
66600 TAAAAAGAT-ATT-TAT
1 TAAAAAGATAATTATAT
66615 TAAAAA
1 TAAAAA
66621 AAATTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAAAAGATAATTATAT
Found at i:70092 original size:67 final size:67
Alignment explanation
Indices: 69977--70299 Score: 351
Period size: 67 Copynumber: 5.0 Consensus size: 67
69967 GGTTTTTTAA
*
69977 GGTAAACTA-CCTATTTGGT--C-T-TATATTTCTAA-TTATGTTTTGGCCACTCGATTATTATT
1 GGTAAACTAGCCTATTTGGTCACTTATATATTTCTAATTTATGTTTTGGTCACTCGATTATTATT
70036 AG
66 AG
* * * *
70038 GGTAAACT-GTCTGTTTTGTCACTTATATATTGTCTAATTTATGTTTTGATCACTCGATTATTAT
1 GGTAAACTAGCCTATTTGGTCACTTATATATT-TCTAATTTATGTTTTGGTCACTCGATTATTAT
70102 TAG
65 TAG
* *
70105 GGTAAACTA-CCAATTTGGTCACTTATATATCTTCTAATTTATG-TTTGGTCACTCGATAATTAT
1 GGTAAACTAGCCTATTTGGTCACTTATATAT-TTCTAATTTATGTTTTGGTCACTCGATTATTA-
70168 TTAG
64 TTAG
**
70172 GGTAAACTAG-CTATTTGGTCACTTATATATTATCTAA--TA--TAAT--TCA-T--ATATATTT
1 GGTAAACTAGCCTATTTGGTCACTTATATATT-TCTAATTTATGTTTTGGTCACTCGAT-TA-TT
70227 ATATAG
63 AT-TAG
*
70233 GGTAAACTACCCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTAT
1 GGTAAACTAGCCTATTTGGTCACTTATATATT-TCTAATTTATGTTTTGGTCACTCGATTATTAT
70298 TA
65 TA
70300 TTTTTTTAAA
Statistics
Matches: 218, Mismatches: 18, Indels: 45
0.78 0.06 0.16
Matches are distributed among these distances:
59 2 0.01
60 2 0.01
61 31 0.14
62 30 0.14
63 1 0.00
64 4 0.02
65 8 0.04
66 25 0.11
67 100 0.46
68 6 0.03
69 5 0.02
70 2 0.01
71 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (67 bp):
GGTAAACTAGCCTATTTGGTCACTTATATATTTCTAATTTATGTTTTGGTCACTCGATTATTATT
AG
Done.