Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001677.1 Hibiscus syriacus cultivar Beakdansim tig00003354_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: 162409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:142272 original size:19 final size:19
Alignment explanation
Indices: 142234--142272 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
142224 ATTAAATAGT
* **
142234 AAAATTAATATTTTCTATA
1 AAAAGTAATATTTTAAATA
142253 AAAAGTAATATTTTAAATA
1 AAAAGTAATATTTTAAATA
142272 A
1 A
142273 GATTTTACCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAAGTAATATTTTAAATA
Found at i:142411 original size:176 final size:175
Alignment explanation
Indices: 142118--142493 Score: 707
Period size: 176 Copynumber: 2.1 Consensus size: 175
142108 ATTTGTTATC
142118 AAAAATATTAATATTTTTTAAAATTTTTAGTAAATTGTTATTTAAAATATTTTTTATTGGAATTA
1 AAAAATATTAATATTTTTTAAAATTTTTAGTAAATTGTTATTTAAAATATTTTTTATTGGAATTA
*
142183 TTAATATTGGGTATTATTTAAAATATTATATTTTACTAAAAATTAAATAGTAAAATTAATATTTT
66 TTAATATTGAGTATTATTTAAAATATTATATTTTACTAAAAATTAAATAGTAAAATTAATATTTT
*
142248 CTATAAAAAGTAATATTTTAAATAAGATTTTACCGTTAATATTAA
131 CGATAAAAAGTAATATTTTAAATAAGATTTTACCGTTAATATTAA
*
142293 AAAAATATTAATATTTTTTAAAATTTTTAGTAAATTGTTATTTTAAATATTTTTTTATTGGAATT
1 AAAAATATTAATATTTTTTAAAATTTTTAGTAAATTGTTATTTAAAATA-TTTTTTATTGGAATT
142358 ATTAATATTGAGTATTATTTAAAATATTATATTTTACTAAAAATTAAATAGTAAAATTAATATTT
65 ATTAATATTGAGTATTATTTAAAATATTATATTTTACTAAAAATTAAATAGTAAAATTAATATTT
142423 TCGATAAAAAGTAATATTTTAAATAAGATTTTACCGTTAATATTAA
130 TCGATAAAAAGTAATATTTTAAATAAGATTTTACCGTTAATATTAA
*
142469 AAAAATATTAATATTTTTTATAATT
1 AAAAATATTAATATTTTTTAAAATT
142494 ATTTTATTTA
Statistics
Matches: 196, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
175 48 0.24
176 148 0.76
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (175 bp):
AAAAATATTAATATTTTTTAAAATTTTTAGTAAATTGTTATTTAAAATATTTTTTATTGGAATTA
TTAATATTGAGTATTATTTAAAATATTATATTTTACTAAAAATTAAATAGTAAAATTAATATTTT
CGATAAAAAGTAATATTTTAAATAAGATTTTACCGTTAATATTAA
Found at i:142448 original size:19 final size:19
Alignment explanation
Indices: 142410--142448 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
142400 ATTAAATAGT
* **
142410 AAAATTAATATTTTCGATA
1 AAAAGTAATATTTTAAATA
142429 AAAAGTAATATTTTAAATA
1 AAAAGTAATATTTTAAATA
142448 A
1 A
142449 GATTTTACCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAAGTAATATTTTAAATA
Found at i:143126 original size:31 final size:31
Alignment explanation
Indices: 143089--143171 Score: 166
Period size: 31 Copynumber: 2.7 Consensus size: 31
143079 TGATAGTTGA
143089 ATATAGTGTAGGGATAAAAGACAAATGGACT
1 ATATAGTGTAGGGATAAAAGACAAATGGACT
143120 ATATAGTGTAGGGATAAAAGACAAATGGACT
1 ATATAGTGTAGGGATAAAAGACAAATGGACT
143151 ATATAGTGTAGGGATAAAAGA
1 ATATAGTGTAGGGATAAAAGA
143172 AGAATATATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.46, C:0.05, G:0.27, T:0.23
Consensus pattern (31 bp):
ATATAGTGTAGGGATAAAAGACAAATGGACT
Found at i:145570 original size:26 final size:25
Alignment explanation
Indices: 145528--145578 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
145518 TAATAAACTT
145528 AATATATATTTAAAAAA-CTATATAA
1 AATATATATTTAAAAAATC-ATATAA
**
145553 AATATTATATTTTCAAAATCATATAA
1 AATA-TATATTTAAAAAATCATATAA
145579 TATGTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 17 0.77
27 1 0.05
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATATATTTAAAAAATCATATAA
Found at i:145604 original size:24 final size:23
Alignment explanation
Indices: 145562--145661 Score: 82
Period size: 24 Copynumber: 4.4 Consensus size: 23
145552 AAATATTATA
*
145562 TTTTCAAAATCATAT--AATATG
1 TTTTCAAAATTATATACAATATG
145583 TTTTCAAAATTATATAACAATATG
1 TTTTCAAAATTATAT-ACAATATG
* * *
145607 TTTTTAAAA--ACTATACTATATA
1 TTTTCAAAATTA-TATACAATATG
**
145629 TTTTCAAAAATTATATATTATATG
1 TTTTC-AAAATTATATACAATATG
*
145653 TTTTTAAAA
1 TTTTCAAAA
145662 ACCGTTTTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
21 14 0.22
22 11 0.17
23 11 0.17
24 27 0.42
25 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (23 bp):
TTTTCAAAATTATATACAATATG
Found at i:145632 original size:22 final size:21
Alignment explanation
Indices: 145602--145663 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
145592 TTATATAACA
*
145602 ATATGTTTTTAAAAACTATACT
1 ATATATTTTTAAAAACTATA-T
* *
145624 ATATATTTTCAAAAATTATAT
1 ATATATTTTTAAAAACTATAT
145645 ATTATATGTTTTTAAAAAC
1 A-TATA--TTTTTAAAAAC
145664 CGTTTTAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 21 0.66
24 9 0.28
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (21 bp):
ATATATTTTTAAAAACTATAT
Found at i:145662 original size:24 final size:24
Alignment explanation
Indices: 145573--145662 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 24
145563 TTTCAAAATC
*
145573 ATATAATATG-TTTTCAAAATTAT
1 ATATAATATGTTTTTAAAAATTAT
* *
145596 ATAACAATATGTTTTTAAAAACTAT
1 AT-ATAATATGTTTTTAAAAATTAT
*
145621 ACTAT-ATA--TTTTCAAAAATTAT
1 A-TATAATATGTTTTTAAAAATTAT
*
145643 ATATTATATGTTTTTAAAAA
1 ATATAATATGTTTTTAAAAA
145663 CCGTTTTAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
21 3 0.06
22 16 0.30
23 2 0.04
24 19 0.35
25 13 0.24
26 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (24 bp):
ATATAATATGTTTTTAAAAATTAT
Found at i:148982 original size:15 final size:15
Alignment explanation
Indices: 148958--148987 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
148948 GAACAAATAA
*
148958 TTGTAGTAATTTTAC
1 TTGTAATAATTTTAC
148973 TTGTAATAATTTTAC
1 TTGTAATAATTTTAC
148988 AATTTTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (15 bp):
TTGTAATAATTTTAC
Found at i:152997 original size:23 final size:23
Alignment explanation
Indices: 152967--153020 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
152957 ATATGCATAA
*
152967 TGCCCGATCACACGACGAATTGT
1 TGCCCGATCAAACGACGAATTGT
*
152990 TGCCCGATCAAATGACGAATTGT
1 TGCCCGATCAAACGACGAATTGT
153013 TGCCCGAT
1 TGCCCGAT
153021 GCTACAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (23 bp):
TGCCCGATCAAACGACGAATTGT
Found at i:156163 original size:30 final size:31
Alignment explanation
Indices: 156124--156196 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
156114 AATGGATTTA
* *
156124 TTTA-GTGACCAAATTATAAA-TTTGGTAAAG
1 TTTAGGTGACCAAAGTATAAACTTT-GAAAAG
156154 TTT-GGTGACCAAAGTATAAACTTTGAAAAG
1 TTTAGGTGACCAAAGTATAAACTTTGAAAAG
156184 TTTAGG-GACCAAA
1 TTTAGGTGACCAAA
156197 ATGTAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 33 0.87
31 5 0.13
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (31 bp):
TTTAGGTGACCAAAGTATAAACTTTGAAAAG
Found at i:157191 original size:30 final size:31
Alignment explanation
Indices: 157146--157217 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
157136 TCTACAGGCC
*
157146 TTAGAAAA-TTTGGGGACC-ATTTGGTAATT
1 TTAGAAAAGTTAGGGGACCAATTTGGTAATT
*
157175 TTTGAAAAGTTAGGGGACCAATTTGGTAATT
1 TTAGAAAAGTTAGGGGACCAATTTGGTAATT
157206 TTAGAAAAGTTA
1 TTAGAAAAGTTA
157218 TGAATGTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 7 0.18
30 9 0.24
31 22 0.58
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (31 bp):
TTAGAAAAGTTAGGGGACCAATTTGGTAATT
Done.