Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003577.1 Hibiscus syriacus cultivar Beakdansim tig00007550_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: 203375
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:172931 original size:29 final size:29
Alignment explanation
Indices: 172892--173001 Score: 204
Period size: 29 Copynumber: 3.8 Consensus size: 29
172882 TATGTGATAT
172892 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
172922 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
172951 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
172980 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
173002 ACATATAGAA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.09
29 68 0.85
30 5 0.06
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:173104 original size:15 final size:15
Alignment explanation
Indices: 173086--173119 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
173076 GAGGGTATAA
173086 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
173101 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
173116 TAGT
1 TAGT
173120 GGTCCTATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:175199 original size:21 final size:21
Alignment explanation
Indices: 175143--175192 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
175133 TTAACGGCTG
* *
175143 CATCATAGCGTTTTTTAAGGT
1 CATCATAGCATTTTTCAAGGT
175164 CATCATAGCATTTTTCAAGGT
1 CATCATAGCATTTTTCAAGGT
175185 CATCATAG
1 CATCATAG
175193 TTATTTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (21 bp):
CATCATAGCATTTTTCAAGGT
Found at i:181813 original size:3 final size:3
Alignment explanation
Indices: 181800--181847 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
181790 AAACTAGCAC
* * *
181800 TTA TT- TTA TTA TTA TTA TTA TTA TTA TAA TAA ATA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
181846 TT
1 TT
181848 CTATTAATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:181861 original size:29 final size:31
Alignment explanation
Indices: 181801--181875 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
181791 AACTAGCACT
*
181801 TATTTTATTATTATTATTATTATTATAATAAA
1 TATTTTATTATTATTACTATTA-TATAATAAA
*
181833 TATTTTATTATTATT-CTATTA-ATAGTAAA
1 TATTTTATTATTATTACTATTATATAATAAA
* * *
181862 AACTTCATTATTAT
1 TATTTTATTATTAT
181876 GCATGGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 18 0.47
31 5 0.13
32 15 0.39
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (31 bp):
TATTTTATTATTATTACTATTATATAATAAA
Found at i:184694 original size:63 final size:64
Alignment explanation
Indices: 184535--184697 Score: 170
Period size: 63 Copynumber: 2.6 Consensus size: 64
184525 GTATGCTTAT
* * * * * *
184535 TATACACGCAGGCATGGCACAAACTGATG-TGTGATTTGTGTCTACGTGTAATCCGGTGATGTAA
1 TATACATGCATGCATGGCACAAACTGATGATGTGA-CTGTATCTACGTGTAATCCGATGATATAA
* ** * * * *
184599 GATACATTTATGCATGGCGCAAACCGAT-ATGTGACTGTATCTATGTGTAATCCGATGGTATAA
1 TATACATGCATGCATGGCACAAACTGATGATGTGACTGTATCTACGTGTAATCCGATGATATAA
*
184662 TATACATGCATGCATGTCACAAACTG-TGATGTGACT
1 TATACATGCATGCATGGCACAAACTGATGATGTGACT
184698 TGTGTCTGTG
Statistics
Matches: 78, Mismatches: 19, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
62 1 0.01
63 51 0.65
64 26 0.33
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
TATACATGCATGCATGGCACAAACTGATGATGTGACTGTATCTACGTGTAATCCGATGATATAA
Found at i:188038 original size:60 final size:60
Alignment explanation
Indices: 187973--188085 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
187963 ATGACTATCC
* *
187973 TTCTAAATTAGTTC-TCAAAC-TTTTGAACATTTCAACTTT-ATCCCCAAACTATAACCTTTA
1 TTCTAAATTAGTCCAT-AAACTTTTTGAACA-TTCAAATTTCAT-CCCAAACTATAACCTTTA
188033 TTCTAAATTAGTCCATAAACTTTTTGAACATTCAAATTTCATCCCAAACTATA
1 TTCTAAATTAGTCCATAAACTTTTTGAACATTCAAATTTCATCCCAAACTATA
188086 TGTATATACT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
60 36 0.75
61 12 0.25
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (60 bp):
TTCTAAATTAGTCCATAAACTTTTTGAACATTCAAATTTCATCCCAAACTATAACCTTTA
Found at i:188329 original size:61 final size:59
Alignment explanation
Indices: 188221--188393 Score: 172
Period size: 61 Copynumber: 2.9 Consensus size: 59
188211 TGGGGATACC
* *
188221 ATTAGAATATTCAAAAGTTTGGGGACCAATTTAGAAA-GAGAGA-CATAGTTTAGGGATGAA
1 ATTAGAAT-TTCAAAAGTTTAGGGACTAATTTA-AAATGAGA-ATCATAGTTTAGGGATGAA
*
188281 ATTAGAATGTTCAAAAAGTTTAGGGACTAATTTAAAATGAGAATCATAGTTTGGGGATGAA
1 ATTAGAAT-TTC-AAAAGTTTAGGGACTAATTTAAAATGAGAATCATAGTTTAGGGATGAA
* * ** * * *
188342 AATAGAATATCCAAAAGTTTAAAGA-TCAATTTAAAATAAGAGTTATAGTTTA
1 ATTAGAAT-TTCAAAAGTTTAGGGACT-AATTTAAAATGAGAATCATAGTTTA
188394 TAGACATATG
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.01
60 47 0.49
61 48 0.50
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (59 bp):
ATTAGAATTTCAAAAGTTTAGGGACTAATTTAAAATGAGAATCATAGTTTAGGGATGAA
Found at i:188390 original size:60 final size:61
Alignment explanation
Indices: 188264--188393 Score: 156
Period size: 60 Copynumber: 2.1 Consensus size: 61
188254 GAAAGAGAGA
* * ** *
188264 CATAGTTTAGGGATGAAATTAGAATGTTCAAAAAGTTTAGGGACTAATTTAAAATGAGAAT
1 CATAGTTTAGGGATGAAAATAGAATGATCAAAAAGTTTAAAGACTAATTTAAAATAAGAAT
* * *
188325 CATAGTTTGGGGATGAAAATAGAAT-ATCCAAAAGTTTAAAGA-TCAATTTAAAATAAGAGT
1 CATAGTTTAGGGATGAAAATAGAATGATCAAAAAGTTTAAAGACT-AATTTAAAATAAGAAT
*
188385 TATAGTTTA
1 CATAGTTTA
188394 TAGACATATG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 34 0.59
61 23 0.40
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (61 bp):
CATAGTTTAGGGATGAAAATAGAATGATCAAAAAGTTTAAAGACTAATTTAAAATAAGAAT
Done.