Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006189.1 Hibiscus syriacus cultivar Beakdansim tig00014728_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: 980383
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 7 of 7
Found at i:946504 original size:29 final size:30
Alignment explanation
Indices: 946472--946535 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
946462 AATATGTAAT
*
946472 AATAAATAATAATAA-AATAATAAGATAAC
1 AATAAATAATAATAATAATAATAAAATAAC
946501 AAT-AATAATAATAATAATAATAAAATAAC
1 AATAAATAATAATAATAATAATAAAATAAC
*
946530 GATAAA
1 AATAAA
946536 AAAACCCGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 11 0.35
29 18 0.58
30 2 0.06
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (30 bp):
AATAAATAATAATAATAATAATAAAATAAC
Found at i:947300 original size:3 final size:3
Alignment explanation
Indices: 947292--947323 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
947282 TGTGGATAGG
947292 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
947324 AGCTGTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:949139 original size:21 final size:21
Alignment explanation
Indices: 949113--949159 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
949103 ACCATATATT
*
949113 ATTTAGGGGTTTTCCACGTAA
1 ATTTAGGGGTCTTCCACGTAA
* *
949134 ATTTA-GTGTCTTCTACGTAA
1 ATTTAGGGGTCTTCCACGTAA
949154 ATTTAG
1 ATTTAG
949160 TGTCTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.43
Consensus pattern (21 bp):
ATTTAGGGGTCTTCCACGTAA
Found at i:949153 original size:20 final size:20
Alignment explanation
Indices: 949128--949167 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
949118 GGGGTTTTCC
949128 ACGTAAATTTAGTGTCTTCT
1 ACGTAAATTTAGTGTCTTCT
949148 ACGTAAATTTAGTGTCTTCT
1 ACGTAAATTTAGTGTCTTCT
949168 TTATCTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (20 bp):
ACGTAAATTTAGTGTCTTCT
Found at i:959015 original size:14 final size:15
Alignment explanation
Indices: 958998--959026 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
958988 AAAAGTAAAT
958998 CATAAAAA-ACTTAA
1 CATAAAAAGACTTAA
959012 CATAAAAAGACTTAA
1 CATAAAAAGACTTAA
959027 TACTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.14, G:0.03, T:0.21
Consensus pattern (15 bp):
CATAAAAAGACTTAA
Found at i:959337 original size:15 final size:15
Alignment explanation
Indices: 959318--959347 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
959308 TATTTATAGG
959318 ATTTTTTATA-ATTT
1 ATTTTTTATACATTT
959332 ATTTTTTATACATTT
1 ATTTTTTATACATTT
959347 A
1 A
959348 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTTATACATTT
Found at i:960300 original size:14 final size:14
Alignment explanation
Indices: 960281--960307 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
960271 TATGAGTTGA
960281 ATTCATACATACAC
1 ATTCATACATACAC
960295 ATTCATACATACA
1 ATTCATACATACA
960308 TGCATTAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTCATACATACAC
Found at i:965287 original size:20 final size:21
Alignment explanation
Indices: 965251--965301 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
965241 TGTTGAAGAG
* *
965251 GTATCGATA-TTGTAAGGGTA
1 GTATCGATACCTGTAAGGATA
*
965271 GTATCGATACCTG-AAGGATG
1 GTATCGATACCTGTAAGGATA
965291 GTATCGATACC
1 GTATCGATACC
965302 CTTAAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (21 bp):
GTATCGATACCTGTAAGGATA
Found at i:965413 original size:54 final size:53
Alignment explanation
Indices: 965271--965415 Score: 191
Period size: 54 Copynumber: 2.7 Consensus size: 53
965261 TGTAAGGGTA
* *
965271 GTATCGATACCTGAAGGATGGTATCGATACCCTTAAAACATCGAATGCCAGATTG
1 GTATCGGTACCTG-AGGAT-GTATCGATACCCTTGAAACATCGAATGCCAGATTG
* * * **
965326 GTATCGGTACCTTGAGGAGGTATCGATACCCTTGAAACATCGAATTCTATTTTG
1 GTATCGGTACC-TGAGGATGTATCGATACCCTTGAAACATCGAATGCCAGATTG
965380 GTATCGGTACCATGAGGATGTATCGATACCCTTGAA
1 GTATCGGTACC-TGAGGATGTATCGATACCCTTGAA
965416 GGGAAGTATC
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
54 64 0.80
55 14 0.17
56 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (53 bp):
GTATCGGTACCTGAGGATGTATCGATACCCTTGAAACATCGAATGCCAGATTG
Found at i:966022 original size:23 final size:23
Alignment explanation
Indices: 965992--966081 Score: 116
Period size: 23 Copynumber: 4.0 Consensus size: 23
965982 TTCGGGACAA
965992 ATATGTGGCACTTCGGTGCAAAT
1 ATATGTGGCACTTCGGTGCAAAT
*
966015 ATATGTGGCACTTCGGTGCAAAC
1 ATATGTGGCACTTCGGTGCAAAT
*
966038 CTATGTGGTC-CTTCGG-G-ACAAT
1 ATATGTGG-CACTTCGGTGCA-AAT
966060 -TATGTGGCACTTCGGTGCAAAT
1 ATATGTGGCACTTCGGTGCAAAT
966082 TACGAGCTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.24
22 7 0.12
23 36 0.61
24 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
ATATGTGGCACTTCGGTGCAAAT
Found at i:966537 original size:20 final size:20
Alignment explanation
Indices: 966500--966539 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
966490 CCTTTTGGTA
*
966500 TTTATGTAAATTATTATGTT
1 TTTATGTAAATAATTATGTT
966520 TTTATGTAAA-AATGTATGTT
1 TTTATGTAAATAAT-TATGTT
966540 AAATGGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (20 bp):
TTTATGTAAATAATTATGTT
Found at i:967396 original size:15 final size:15
Alignment explanation
Indices: 967346--967408 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
967336 CTACCATTAC
*
967346 CTCCACCACCATCAT
1 CTCCACCACCACCAT
* * * * *
967361 CTTCACTACTATCAC
1 CTCCACCACCACCAT
967376 CTCCACCACCACCAT
1 CTCCACCACCACCAT
*
967391 CTCCACCGCCACCAT
1 CTCCACCACCACCAT
967406 CTC
1 CTC
967409 AGCTAGTTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.24, C:0.54, G:0.02, T:0.21
Consensus pattern (15 bp):
CTCCACCACCACCAT
Found at i:971402 original size:17 final size:18
Alignment explanation
Indices: 971360--971403 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
971350 AAATATCATA
971360 AAACCCCCTAAATTTTAT
1 AAACCCCCTAAATTTTAT
971378 AAACCCCCTAAATTTTAT
1 AAACCCCCTAAATTTTAT
971396 AAACCCCC
1 AAACCCCC
971404 AAAACTTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.27
Consensus pattern (18 bp):
AAACCCCCTAAATTTTAT
Found at i:971888 original size:20 final size:20
Alignment explanation
Indices: 971863--971904 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
971853 CTAATGAGAG
971863 TTGAGATTAGGGTTAGGGAT
1 TTGAGATTAGGGTTAGGGAT
971883 TTGAGATTAGGGTTAGGGAT
1 TTGAGATTAGGGTTAGGGAT
971903 TT
1 TT
971905 AAGTTTAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (20 bp):
TTGAGATTAGGGTTAGGGAT
Found at i:971912 original size:20 final size:20
Alignment explanation
Indices: 971866--971912 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
971856 ATGAGAGTTG
*
971866 AGATTAGGGTTAGGGATTTG
1 AGATTAGGGTTAGGGATTTA
971886 AGATTAGGGTTAGGGATTTA
1 AGATTAGGGTTAGGGATTTA
*
971906 AGTTTAG
1 AGATTAG
971913 AGATTTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.36, T:0.36
Consensus pattern (20 bp):
AGATTAGGGTTAGGGATTTA
Done.