Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003068.1 Hibiscus syriacus cultivar Beakdansim tig00006395_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: 55025
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1638 original size:22 final size:22
Alignment explanation
Indices: 1575--1638 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
1565 TTTTGAATAT
* *
1575 ATATTATATAAATTTA-ATTTAA
1 ATATAATATAAA-TTACATTAAA
* *
1597 ATAAAATA-AAATAACTATTAAA
1 ATATAATATAAATTAC-ATTAAA
1619 ATATAATATAAATTACATTA
1 ATATAATATAAATTACATTA
1639 TTCCTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 2 0.06
21 3 0.09
22 22 0.67
23 6 0.18
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATAATATAAATTACATTAAA
Found at i:2729 original size:45 final size:44
Alignment explanation
Indices: 2677--2767 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 44
2667 ATACTTTAAA
*
2677 TGTACAATTAA-AAAAGTGACCGAAGTTGAAGACTTATTTTTTCTT
1 TGTACAATTAACAAAAGTGACCGAAGTTAAAGACTT-TTTTTT-TT
*
2722 TGTACAATTAACAAAAGTTACCGAAGTTAAAGACTTTTTTTTTT
1 TGTACAATTAACAAAAGTGACCGAAGTTAAAGACTTTTTTTTTT
2766 TG
1 TG
2768 CCATTATACC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 4 0.09
45 17 0.40
46 22 0.51
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (44 bp):
TGTACAATTAACAAAAGTGACCGAAGTTAAAGACTTTTTTTTTT
Found at i:23217 original size:2 final size:2
Alignment explanation
Indices: 23210--23244 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23200 TTAAGGATAA
23210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23245 AATTTGGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24301 original size:15 final size:17
Alignment explanation
Indices: 24271--24302 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
24261 AAACATTATC
24271 TTATCTTTAGTTTATTA
1 TTATCTTTAGTTTATTA
24288 TTAT-TTTA-TTTATTA
1 TTATCTTTAGTTTATTA
24303 AACTACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TTATCTTTAGTTTATTA
Found at i:25214 original size:28 final size:28
Alignment explanation
Indices: 25187--25241 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
25177 ATTAGTAATA
*
25187 ATTAATAATTTAAT-AATAATTTTAAAT
1 ATTAAGAATTTAATCAATAATTTTAAAT
* * *
25214 ATTAGGAATTTATTCAATTATTTTAAAT
1 ATTAAGAATTTAATCAATAATTTTAAAT
25242 TAGGACTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (28 bp):
ATTAAGAATTTAATCAATAATTTTAAAT
Found at i:28514 original size:14 final size:13
Alignment explanation
Indices: 28490--28522 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
28480 TAAAATTATT
28490 TATTAAATAATAA
1 TATTAAATAATAA
28503 TATTATAATAATAA
1 TATTA-AATAATAA
28517 TATTAA
1 TATTAA
28523 TAAAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATTAAATAATAA
Found at i:43350 original size:21 final size:22
Alignment explanation
Indices: 43289--43351 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 22
43279 TGTCATAACC
*
43289 ATTTTTTAAAACAATTAATATT
1 ATTTTTTAAAACAATTATTATT
** *
43311 ATTTTATTATATTCTATTATTATT
1 ATTTT-TTA-AAACAATTATTATT
43335 -TTTTTTAAAACAATTAT
1 ATTTTTTAAAACAATTAT
43352 GACTTTAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
21 7 0.22
22 8 0.25
23 7 0.22
24 10 0.31
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTTAAAACAATTATTATT
Found at i:43481 original size:16 final size:16
Alignment explanation
Indices: 43456--43498 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
43446 AACGTCTTTT
43456 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
43472 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
43489 ACAAAAATTT
1 AAAAAAATTT
43499 GGTCTGCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:46248 original size:26 final size:25
Alignment explanation
Indices: 46133--46256 Score: 198
Period size: 25 Copynumber: 5.0 Consensus size: 25
46123 AGTTAGGGGA
*
46133 TTAGGG-TTGAAACCCTAAATTG-T
1 TTAGGGTTTGAAACCCTAAACTGAT
*
46156 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
46181 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
46206 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
46231 TTAGGGTTTTGAAACCCTAATCTGAT
1 TTAGGG-TTTGAAACCCTAAACTGAT
46257 GGGTTGGTTC
Statistics
Matches: 94, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
23 6 0.06
24 14 0.15
25 56 0.60
26 18 0.19
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:46427 original size:15 final size:15
Alignment explanation
Indices: 46382--46427 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
46372 AATATATAAT
46382 TTAATAATAATAATAA
1 TTAATAATAATAA-AA
46398 -TAATAATTAATAAAA
1 TTAATAA-TAATAAAA
46413 TTAAATAAT-ATAAAA
1 TT-AATAATAATAAAA
46428 AAGACCCGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 14 0.52
16 8 0.30
17 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAATAATAATAAAA
Found at i:46649 original size:43 final size:43
Alignment explanation
Indices: 46602--46886 Score: 136
Period size: 40 Copynumber: 6.4 Consensus size: 43
46592 AATGAAAAGG
46602 TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAAGAAA
1 TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAAGAAA
* * **
46645 TCT-G--GTC-AAGGGATGACACGGCTCATACGCGATGAAGAGT
1 TCTGGTCGTCTAAGGG-TGACACGGCTCCTACGTGATGAAGAAA
* * * * *
46685 TATGGTCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAA
1 TCTGGTCGTC--T---AAGGGTG---ACACGGCTCCTACGTGATGAAGAAA
* * **
46736 TCT-G--GTC-AAGGGATGACACGGCTCATACGCGATGAAGAGT
1 TCTGGTCGTCTAAGGG-TGACACGGCTCCTACGTGATGAAGAAA
* * * *
46776 TCTGGTCATCTTTAAGAAGGGTGATAATTCGGTTCCTACGTGATGAGGAAA
1 TCTGGTCGTC--T---AAGGGTGA-CA--CGGCTCCTACGTGATGAAGAAA
* * ** * * *
46827 TCCGATTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAG
1 TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAAGAAA
46870 TCTGGTCGTCTAAGGGT
1 TCTGGTCGTCTAAGGGT
46887 AGATGACATG
Statistics
Matches: 174, Mismatches: 42, Indels: 52
0.65 0.16 0.19
Matches are distributed among these distances:
39 5 0.03
40 49 0.28
41 2 0.01
42 6 0.03
43 41 0.24
45 1 0.01
46 7 0.04
48 7 0.04
49 12 0.07
50 1 0.01
51 43 0.25
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (43 bp):
TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAAGAAA
Found at i:46782 original size:91 final size:91
Alignment explanation
Indices: 46627--46828 Score: 377
Period size: 91 Copynumber: 2.2 Consensus size: 91
46617 GTGACACGGC
*
46627 TCCTACGTGATGAAGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTATGGTC
1 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTATGGTC
46692 ATCTTTAAGAAGGGTGATAACTCGGT
66 ATCTTTAAGAAGGGTGATAACTCGGT
*
46718 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
1 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTATGGTC
*
46783 ATCTTTAAGAAGGGTGATAATTCGGT
66 ATCTTTAAGAAGGGTGATAACTCGGT
46809 TCCTACGTGATGAGGAAATC
1 TCCTACGTGATGAGGAAATC
46829 CGATTATCTA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 108 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (91 bp):
TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTATGGTC
ATCTTTAAGAAGGGTGATAACTCGGT
Found at i:46965 original size:141 final size:134
Alignment explanation
Indices: 46718--47018 Score: 343
Period size: 141 Copynumber: 2.2 Consensus size: 134
46708 ATAACTCGGT
* ** *
46718 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
1 TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTGGCC
*
46783 ATCTTTAAGAAGGGTGATAATTCGGTTCCTACGTGATGAGGAAATCCGATTATCTAAGGTTGACA
66 ATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAATCCGATTATCTAAGGTTGACA
46848 CGGC
131 CGGC
* * * *
46852 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
1 TCCTACGTGATGAGGAAATCT-G--GTC-AA-GG--GATGACACGGCTCATACACGATGAAGAAC
* *** * *
46917 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
59 TCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAATCCGATTAT-CTAA
* *
46982 TGTTGACAC-TC
123 GGTTGACACGGC
* * *
46993 TCCTATGTGATAAGGAGATCTGGTCA
1 TCCTACGTGATGAGGAAATCTGGTCA
47019 GTTGATGTTG
Statistics
Matches: 138, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
134 20 0.14
135 1 0.01
137 4 0.03
138 5 0.04
139 2 0.01
140 1 0.01
141 93 0.67
142 12 0.09
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (134 bp):
TCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTGGCC
ATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGAAATCCGATTATCTAAGGTTGACA
CGGC
Found at i:47987 original size:7 final size:8
Alignment explanation
Indices: 47959--47994 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
47949 TCCTTTATTT
47959 ATTTTTTC
1 ATTTTTTC
47967 -TTCTTTTC
1 ATT-TTTTC
47975 ATTTTTTC
1 ATTTTTTC
47983 ATTTTTTC
1 ATTTTTTC
47991 ATTT
1 ATTT
47995 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 2 0.08
8 22 0.85
9 2 0.08
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTTC
Done.