Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007822.1 Hibiscus syriacus cultivar Beakdansim tig00110159_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: 1828853
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1791684 original size:335 final size:333
Alignment explanation
Indices: 1791068--1791722 Score: 1067
Period size: 335 Copynumber: 2.0 Consensus size: 333
1791058 AGTAATGAAA
*
1791068 AAAACATGTTAATATGGGTTTACAAAATAATGGGGAGCTCCCAAGTACATAAAAAATACTACAAA
1 AAAACATGATAATATGGGTTTACAAAATAATGGGGAGCTCCCAAGTACATAAAAAATACTACAAA
* *
1791133 TATCGAGTATCAAAAGAGTTATAAGTGAATACATAAAAGGGTTCATATATAGTATATGCCCTCTA
66 TATCGAGTATCAAAAGAGTTATAAGTGAATACATAAAAGGGTTCATAAATAGTACATGCCCTCTA
*
1791198 AAGATGACTCAAGACGTACTCTAGTGGTCACTACTGGTCTGTACTGCTGCACTGGAATATCTGGC
131 AAGATGACTCAAGACGTACTCTAGTGGTCACTACTGGTCTGTACTGCCGCACTGGAATATCTGGC
* * *
1791263 GACTATAACTCACCACAATATGCCCCTAAAAACTTGTGCACAGAAACACATTCTAAACACTGAGC
196 GACGATAACTCACCACAACATGCCCCTAAAAACTTGTGCACAAAAACACATTCTAAACACTGAGC
* * *
1791328 TTGCAAGCTCAGTACCTCACTAATAACTGTATTATACTACATGCATTCACTAAATGAGATTAATA
261 TTACAAGCTCAATACCTCACTAATAACTATATTATACTACATGCATTCACTAAATGAGATTAATA
1791393 ATAAAAAC
326 ATAAAAAC
*
1791401 AAAACATGATAATATGGGTTTATAAAATAATGGGGAGCTCCCCAAGTACATCAAAAAATACTACA
1 AAAACATGATAATATGGGTTTACAAAATAATGGGGAGCT-CCCAAGTACAT-AAAAAATACTACA
1791466 AATATCGAGTATCAAAAGAGTTATAAGTGAATACATAAAAGGGTTCATAAATAGTACATGCCCTC
64 AATATCGAGTATCAAAAGAGTTATAAGTGAATACATAAAAGGGTTCATAAATAGTACATGCCCTC
* * * * *
1791531 TAAAGATGACTTAAGACGTACTCTGGTGGTCACTATTGGTCTGTACTGCCGCACTGGAATGTTTG
129 TAAAGATGACTCAAGACGTACTCTAGTGGTCACTACTGGTCTGTACTGCCGCACTGGAATATCTG
* * * **
1791596 GCGACGATAACTCCCCACGACATGCCCCTAAAAACTTGTGCACAAAAACACATTCTGAACGTTGA
194 GCGACGATAACTCACCACAACATGCCCCTAAAAACTTGTGCACAAAAACACATTCTAAACACTGA
** * *
1791661 GCTTATGAGCTTAATATCTCACTAATAACTATATTATACTACATGCATTCACTAAATGAGAT
259 GCTTACAAGCTCAATACCTCACTAATAACTATATTATACTACATGCATTCACTAAATGAGAT
1791723 AGCTGGTGGA
Statistics
Matches: 295, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
333 37 0.13
334 11 0.04
335 247 0.84
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (333 bp):
AAAACATGATAATATGGGTTTACAAAATAATGGGGAGCTCCCAAGTACATAAAAAATACTACAAA
TATCGAGTATCAAAAGAGTTATAAGTGAATACATAAAAGGGTTCATAAATAGTACATGCCCTCTA
AAGATGACTCAAGACGTACTCTAGTGGTCACTACTGGTCTGTACTGCCGCACTGGAATATCTGGC
GACGATAACTCACCACAACATGCCCCTAAAAACTTGTGCACAAAAACACATTCTAAACACTGAGC
TTACAAGCTCAATACCTCACTAATAACTATATTATACTACATGCATTCACTAAATGAGATTAATA
ATAAAAAC
Found at i:1792249 original size:20 final size:20
Alignment explanation
Indices: 1792222--1792264 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1792212 TCGACACTAA
*
1792222 ACCT-TTGGTGTCGATACCC
1 ACCTGTTGGTATCGATACCC
*
1792241 ACCTGTTGGTATTGATACCC
1 ACCTGTTGGTATCGATACCC
1792261 -CCTG
1 ACCTG
1792265 ACTGATGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.16, C:0.30, G:0.21, T:0.33
Consensus pattern (20 bp):
ACCTGTTGGTATCGATACCC
Found at i:1793077 original size:24 final size:24
Alignment explanation
Indices: 1793045--1793096 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1793035 ATGTTCTAGA
1793045 GGTGCTGAGTTTAATCCTTACCTT
1 GGTGCTGAGTTTAATCCTTACCTT
1793069 GGTGCTGAGTTTAATCCTTACCTT
1 GGTGCTGAGTTTAATCCTTACCTT
1793093 GGTG
1 GGTG
1793097 TTGATGGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.40
Consensus pattern (24 bp):
GGTGCTGAGTTTAATCCTTACCTT
Found at i:1800275 original size:20 final size:20
Alignment explanation
Indices: 1800250--1800316 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1800240 TTCGTACATG
1800250 GATGCACAACAGGATGCATC
1 GATGCACAACAGGATGCATC
* *
1800270 GATGCACAGCAAGATGCATC
1 GATGCACAACAGGATGCATC
* *
1800290 GATGCACATCAGGATGCATT
1 GATGCACAACAGGATGCATC
1800310 GATGCAC
1 GATGCAC
1800317 TAAGTGCATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (20 bp):
GATGCACAACAGGATGCATC
Found at i:1800361 original size:20 final size:19
Alignment explanation
Indices: 1800336--1800392 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
1800326 TCGAAATGGA
1800336 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCA-G
*
1800356 GTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCAC---TGCAG
1800378 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1800393 TTGACACCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
22 14 0.44
23 4 0.12
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (19 bp):
GTGCATGGATGCACTGCAG
Found at i:1800506 original size:30 final size:31
Alignment explanation
Indices: 1800472--1800532 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1800462 AAACTTTGAA
*
1800472 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGACCAAAAACCATTTTG
1800502 TAAATTCAATTCAAGACCAAAAACCATTTTG
1 TAAATTCAATTCAAGACCAAAAACCATTTTG
1800533 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (31 bp):
TAAATTCAATTCAAGACCAAAAACCATTTTG
Found at i:1803689 original size:20 final size:20
Alignment explanation
Indices: 1803664--1803728 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
1803654 GCAGTCTTCG
1803664 TGCATGGATGCACAACAGGA
1 TGCATGGATGCACAACAGGA
* *
1803684 TGCATGGATACACAGCAGGA
1 TGCATGGATGCACAACAGGA
* *
1803704 TGCATCGATGCACATCAGGA
1 TGCATGGATGCACAACAGGA
1803724 TGCAT
1 TGCAT
1803729 CAATGCACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (20 bp):
TGCATGGATGCACAACAGGA
Found at i:1803729 original size:20 final size:20
Alignment explanation
Indices: 1803664--1803736 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1803654 GCAGTCTTCG
*
1803664 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
* * *
1803684 TGCATGGATACACAGCAGGA
1 TGCATCGATGCACAACAGGA
*
1803704 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACAACAGGA
*
1803724 TGCATCAATGCAC
1 TGCATCGATGCAC
1803737 TAAGTGCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:1803780 original size:20 final size:19
Alignment explanation
Indices: 1803755--1803815 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 19
1803745 TTCGAAATGG
1803755 AGTGCATGGATGCACTGCA
1 AGTGCATGGATGCACTGCA
*
1803774 TAGTGCATCGATGCACTAGTGCA
1 -AGTGCATGGATGCAC---TGCA
*
1803797 GGTGCATGGATGCACTGCA
1 AGTGCATGGATGCACTGCA
1803816 GGGGTGTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 4 0.11
20 14 0.40
22 13 0.37
23 4 0.11
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (19 bp):
AGTGCATGGATGCACTGCA
Found at i:1803808 original size:22 final size:21
Alignment explanation
Indices: 1803755--1803834 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 21
1803745 TTCGAAATGG
1803755 AGTGCATGGATGCAC-TGCAT
1 AGTGCATGGATGCACTTGCAT
*
1803775 AGTGCATCGATGCACTAGTGCA-
1 AGTGCATGGATGCACT--TGCAT
* *
1803797 GGTGCATGGATGCAC-TGCAGG
1 AGTGCATGGATGCACTTGCA-T
* *
1803818 GGTGTATGGATGCACTT
1 AGTGCATGGATGCACTT
1803835 TGACACCCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 4 0.08
20 14 0.28
21 14 0.28
22 14 0.28
23 4 0.08
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (21 bp):
AGTGCATGGATGCACTTGCAT
Found at i:1803947 original size:30 final size:31
Alignment explanation
Indices: 1803913--1803973 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1803903 AAACTTTGAA
1803913 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1803943 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1803974 CCTTAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1804560 original size:16 final size:17
Alignment explanation
Indices: 1804534--1804566 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1804524 ATCACCGACC
1804534 AAATTTCACTATTCACA
1 AAATTTCACTATTCACA
1804551 AAATTT-ACTATTCACA
1 AAATTTCACTATTCACA
1804567 TGAATACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTTCACTATTCACA
Found at i:1809067 original size:13 final size:14
Alignment explanation
Indices: 1809033--1809086 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
1809023 AAAATAATTA
*
1809033 AAACAATTAAATAG
1 AAACAATTAAATAC
*
1809047 AAA-TATTAAATAC
1 AAACAATTAAATAC
*
1809060 AAAC-ATTACAATTC
1 AAACAATTA-AATAC
1809074 AAACAATTAAATA
1 AAACAATTAAATA
1809087 ATAATAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 15 0.45
14 14 0.42
15 4 0.12
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.26
Consensus pattern (14 bp):
AAACAATTAAATAC
Found at i:1809586 original size:21 final size:21
Alignment explanation
Indices: 1809560--1809621 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1809550 CCCAACAGTG
1809560 GTGGCATCTGAATCGACTGCA
1 GTGGCATCTGAATCGACTGCA
* * *
1809581 GTGGCATTTGAACCGACTGCG
1 GTGGCATCTGAATCGACTGCA
1809602 GTGGCATCTGAAGT-GACTGC
1 GTGGCATCTGAA-TCGACTGC
1809622 GTTGCCATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (21 bp):
GTGGCATCTGAATCGACTGCA
Found at i:1809634 original size:21 final size:21
Alignment explanation
Indices: 1809595--1809634 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1809585 CATTTGAACC
* *
1809595 GACTGCGGTGGCATCTGAAGT
1 GACTGCGGTGCCATATGAAGT
*
1809616 GACTGCGTTGCCATATGAA
1 GACTGCGGTGCCATATGAA
1809635 ACTACTGTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (21 bp):
GACTGCGGTGCCATATGAAGT
Found at i:1811261 original size:24 final size:23
Alignment explanation
Indices: 1811217--1811261 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1811207 CCCTAATTAA
*
1811217 ATAAATAATATACAAATTAAAAT
1 ATAAATAATATACAAAATAAAAT
1811240 ATAAACTAATACTA-AAAATAAA
1 ATAAA-TAATA-TACAAAATAAA
1811262 TAAAACATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAATAATATACAAAATAAAAT
Found at i:1811437 original size:26 final size:26
Alignment explanation
Indices: 1811402--1811451 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1811392 AAATTAGTAA
1811402 ATTAAATAATAATAAAATAATAAACT
1 ATTAAATAATAATAAAATAATAAACT
* *
1811428 ATTAAATAATTATAATATAATAAA
1 ATTAAATAATAATAAAATAATAAA
1811452 AAAGTATAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
ATTAAATAATAATAAAATAATAAACT
Found at i:1820234 original size:2 final size:2
Alignment explanation
Indices: 1820227--1820276 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1820217 TTGGACGACC
1820227 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1820269 AT AT AT AT
1 AT AT AT AT
1820277 GCATATGCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1826166 original size:22 final size:23
Alignment explanation
Indices: 1826113--1826171 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
1826103 TTCTTTTTAA
* **
1826113 AAAATATAATAAT-TTAAAATTT
1 AAAATATAAAAATATTAAAAAAT
*
1826135 AAAATGTAAAAATATTAAAAAAT
1 AAAATATAAAAATATTAAAAAAT
1826158 -AAATATAAAAATAT
1 AAAATATAAAAATAT
1826172 CATTAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AAAATATAAAAATATTAAAAAAT
Done.