Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007337.1 Hibiscus syriacus cultivar Beakdansim tig00019648_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: 44440
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1307 original size:14 final size:14
Alignment explanation
Indices: 1288--1317 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1278 AGCACCAAAC
1288 TTTTGAAATTAAAT
1 TTTTGAAATTAAAT
*
1302 TTTTGAAATTGAAT
1 TTTTGAAATTAAAT
1316 TT
1 TT
1318 CGTAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (14 bp):
TTTTGAAATTAAAT
Found at i:3448 original size:240 final size:244
Alignment explanation
Indices: 2995--3473 Score: 632
Period size: 240 Copynumber: 2.0 Consensus size: 244
2985 TGTATGTCAT
* * * *
2995 TTACATGGGTTTTTCTTACTCGTATAAGGATGGTGAAACATGTGGAGGTTATGTTCTTAATTTGT
1 TTACATGAGTTTTGCTTACTCGTATAAGGATGGTGAAACATGTGGAGGTTATGTGCTTAATTTAT
* * *
3060 GGTTTAAACATATTGAATGTTACCTTTGTGTAAAAATGATGTATAATGATCCTTAATGATTTTCA
66 GGTTTAAACATATTGAATGTTACCTTTGTGTAAAAATGATG---AATGACCCCTAATGACTTTCA
* *
3125 TAAGCTTTAATAACCAACTTAATTCTTAAAATAAGTGTTTGGGTGAATTTGGGGTATTTCTCGTA
128 TAAGCTTTAATAACCAACTTAAGTCTTAAAATAAGTGTTTGGGTGAATTTGGGGTATTTCCCGTA
*
3190 TGAAACAGTGTATTTCTAGGTTTAAGTATAGATATTAGATGAATTTGGGATA
193 TGAAACAATGTATTTCTAGGTTTAAGTATAGATATTAGATGAATTTGGGATA
* * * *
3242 TTACATGAGTTTTGCTTGCTTGTATAAGGGATGGTGAAACATGTGGCGGTTATGTGCTTGATTTA
1 TTACATGAGTTTTGCTTACTCGTATAA-GGATGGTGAAACATGTGGAGGTTATGTGCTTAATTTA
* * *
3307 TGGTTTGAACAT-TTTAGATGTTACC-TT-TGT-ATAA-GCATG-ATGACCCCTAATGACTTTCA
65 TGGTTTAAACATATTGA-ATGTTACCTTTGTGTAAAAATG-ATGAATGACCCCTAATGACTTTCA
* * *
3366 TAAGCTTT-ATAACTAACTTAAGTCTTAAAAT-AGTGTTTTGGTGAATTTGAGGGTGTTTCCCGT
128 TAAGCTTTAATAACCAACTTAAGTCTTAAAATAAGTGTTTGGGTGAATTTG-GGGTATTTCCCGT
* * *
3429 ATGAAACAATGTATTTCTAGGTTTGAGTATCGATATTGGATGAAT
192 ATGAAACAATGTATTTCTAGGTTTAAGTATAGATATTAGATGAAT
3474 AATATTGATA
Statistics
Matches: 205, Mismatches: 23, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
239 17 0.08
240 73 0.36
241 25 0.12
244 1 0.00
245 6 0.03
246 3 0.01
247 28 0.14
248 52 0.25
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (244 bp):
TTACATGAGTTTTGCTTACTCGTATAAGGATGGTGAAACATGTGGAGGTTATGTGCTTAATTTAT
GGTTTAAACATATTGAATGTTACCTTTGTGTAAAAATGATGAATGACCCCTAATGACTTTCATAA
GCTTTAATAACCAACTTAAGTCTTAAAATAAGTGTTTGGGTGAATTTGGGGTATTTCCCGTATGA
AACAATGTATTTCTAGGTTTAAGTATAGATATTAGATGAATTTGGGATA
Found at i:3521 original size:20 final size:20
Alignment explanation
Indices: 3496--3565 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
3486 ACCAATATTA
*
3496 GAATTACAACATTGATACTG
1 GAATTACAATATTGATACTG
*
3516 GAATTACAATATCGATACTG
1 GAATTACAATATTGATACTG
*
3536 GAATTACAATATTGATATTG
1 GAATTACAATATTGATACTG
*
3556 AAATTACAAT
1 GAATTACAAT
3566 TCAATATCGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (20 bp):
GAATTACAATATTGATACTG
Found at i:6482 original size:30 final size:28
Alignment explanation
Indices: 6428--6493 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
6418 ATATATCTTG
*
6428 TCACATGACTTATATCTATATCATATAA
1 TCACATAACTTATATCTATATCATATAA
* * *
6456 TTACATAACTTATATTGTATTATCATATTA
1 TCACATAACTTATA-TCTA-TATCATATAA
6486 TCACATAA
1 TCACATAA
6494 TCATGTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 12 0.39
29 3 0.10
30 16 0.52
ACGTcount: A:0.39, C:0.15, G:0.03, T:0.42
Consensus pattern (28 bp):
TCACATAACTTATATCTATATCATATAA
Found at i:22982 original size:23 final size:23
Alignment explanation
Indices: 22952--23032 Score: 119
Period size: 23 Copynumber: 3.5 Consensus size: 23
22942 CTCATATAAA
22952 TGCACCGAAGT-TCCACGTAGAAT
1 TGCACCGAAGTGT-CACGTAGAAT
* *
22975 TGCACCGAAATGTCGCGTAGAAT
1 TGCACCGAAGTGTCACGTAGAAT
22998 TGCACCGAAGTGTCACGTAGAAT
1 TGCACCGAAGTGTCACGTAGAAT
*
23021 TGTACCGAAGTG
1 TGCACCGAAGTG
23033 CCATATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
23 51 0.98
24 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
TGCACCGAAGTGTCACGTAGAAT
Found at i:23547 original size:2 final size:2
Alignment explanation
Indices: 23540--23624 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
23530 CAACTCATAG
23540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
23582 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23624 T
1 T
23625 CATTTACCTA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:26421 original size:30 final size:30
Alignment explanation
Indices: 26380--26447 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
26370 ATATATCTTG
*
26380 TCACATGACTTATATCT-TATGATCATATAA
1 TCACATAACTTATAT-TGTATGATCATATAA
* * *
26410 TTACATAACTTATATTGTATTATCATATTA
1 TCACATAACTTATATTGTATGATCATATAA
26440 TCACATAA
1 TCACATAA
26448 TCATGTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (30 bp):
TCACATAACTTATATTGTATGATCATATAA
Found at i:27346 original size:65 final size:63
Alignment explanation
Indices: 27271--27433 Score: 186
Period size: 65 Copynumber: 2.6 Consensus size: 63
27261 ATGAATTAAA
* *
27271 TTGAAA-ATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TT
1 TTGAAACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATT
* * * * *
27333 TATGAAAACATCGAATGTATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTAT
1 T-TG-AAACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATAT
27398 T
63 T
* * *
27399 TTGAAACATCAAATGCACTTGATGTATCGATGCAC
1 TTGAAACATCGAATGCATTTGATGCATCGATGCAC
27434 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 3 0.04
64 30 0.35
65 46 0.54
66 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (63 bp):
TTGAAACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATT
Found at i:35563 original size:65 final size:63
Alignment explanation
Indices: 35494--35648 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 63
35484 AATTGATTAT
* *
35494 CGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACA
1 CGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACA
35558 A
63 A
* * * * * *
35559 CGAATGCATTTGATGTATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACAT
1 CGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACAA
* *
35623 CGAAAGCACTTGATGCATCGATGCAC
1 CGAATGCATTTGATGCATCGATGCAC
35649 TAAGGGTCCA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 1 0.01
64 27 0.35
65 44 0.57
66 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (63 bp):
CGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACAA
Found at i:43021 original size:23 final size:23
Alignment explanation
Indices: 42991--43071 Score: 119
Period size: 23 Copynumber: 3.5 Consensus size: 23
42981 CTCATATAAA
42991 TGCACCGAAGT-TCCACGTAGAAT
1 TGCACCGAAGTGT-CACGTAGAAT
* *
43014 TGCACCGAAATGTCGCGTAGAAT
1 TGCACCGAAGTGTCACGTAGAAT
43037 TGCACCGAAGTGTCACGTAGAAT
1 TGCACCGAAGTGTCACGTAGAAT
*
43060 TGTACCGAAGTG
1 TGCACCGAAGTG
43072 CCATATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
23 51 0.98
24 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
TGCACCGAAGTGTCACGTAGAAT
Found at i:43584 original size:2 final size:2
Alignment explanation
Indices: 43577--43633 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
43567 ACTCATAGTC
43577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
43617 AT AG AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
43634 CATTTTACCT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Done.