Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007357.1 Hibiscus syriacus cultivar Beakdansim tig00019719_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: 81613
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:7185 original size:120 final size:120
Alignment explanation
Indices: 6798--7197 Score: 418
Period size: 120 Copynumber: 3.3 Consensus size: 120
6788 CATTGCTGTT
* * * * * * *
6798 AAAACTTAACACATTTAGT-CTCTAAACTATTATTTTTAG-CTCATTTTAATACTTAAACTTTCA
1 AAAACTTAACGCAATTAGTAC-CTAAACTATAAGTTTTAGTC-CA-TTTAGTACCTAAACTTTTA
* * * * *
6861 TTTTTTTC-AAATCACA-CTTAAAGTTTAGTTTTTGTTTCATTTCAGTACCCACCGTT-
63 ATTTTTTCAAAATCATATC-TAACGTTTAGTTTTTGTTTCATTTTAGTACCCACAGTTA
* * * * * *
6917 AAAACTTAACACATTTAGTACCT-AACTATCATTTTTGGTCCATTTTATTACCTAAACTTTTAAT
1 AAAACTTAACGCAATTAGTACCTAAACTATAAGTTTTAGTCCA-TTTAGTACCTAAACTTTTAAT
* *
6981 TTTTTCAAAATCATGTCTAACATTTAGTTTTTGTTTCATTTTAGTACCCCACAGTTA
65 TTTTTCAAAATCATATCTAACGTTTAGTTTTTGTTTCATTTTAGTA-CCCACAGTTA
* * * *
7038 AAAATTTAATGCAATTAGTACCTAAACTATAAGTTTTAGTCC-TTTAGTATCTATACTTTTAATT
1 AAAACTTAACGCAATTAGTACCTAAACTATAAGTTTTAGTCCATTTAGTACCTAAACTTTTAA-T
* * * * *
7102 TTTTTTAAATTCATATCTAATGTTTAGTTTTTGTTTCATTTTATTACCCACAATTA
65 TTTTTCAAAATCATATCTAACGTTTAGTTTTTGTTTCATTTTAGTACCCACAGTTA
*
7158 AAAACTTAACGCAATTAGTATCTAAACTATAAGTTTTAGT
1 AAAACTTAACGCAATTAGTACCTAAACTATAAGTTTTAGT
7198 ACCTAAACTT
Statistics
Matches: 241, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
118 39 0.16
119 54 0.22
120 73 0.30
121 60 0.25
122 15 0.06
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (120 bp):
AAAACTTAACGCAATTAGTACCTAAACTATAAGTTTTAGTCCATTTAGTACCTAAACTTTTAATT
TTTTCAAAATCATATCTAACGTTTAGTTTTTGTTTCATTTTAGTACCCACAGTTA
Found at i:44302 original size:2 final size:2
Alignment explanation
Indices: 44284--44317 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
44274 AATAATCATC
* *
44284 AT AT CT AT AT AT CT 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
44318 TTGATTAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46958 original size:160 final size:156
Alignment explanation
Indices: 46771--47086 Score: 596
Period size: 160 Copynumber: 2.0 Consensus size: 156
46761 AAATTTATTG
46771 GATTTGTTGTTAAAATATCACATACAAAACTCCCACCGGATGGTCAGACACCCAAGGAAATAAGA
1 GATTTGTTGTTAAAATATCACATACAAAACTCCCACCGGATGGTCAGACACCCAAGGAAATAAGA
46836 CAATCGGGACTTGTCGACATAGTTTTTTTTTTTTTTTTTTGGGTGAACAAGGGAAACAAACCAGA
66 CAATCGGGACTTGTCGACATAG----TTTTTTTTTTTTTTGGGTGAACAAGGGAAACAAACCAGA
46901 TTAGCAATTACAAAACATGGATTTCAGTCA
127 TTAGCAATTACAAAACATGGATTTCAGTCA
46931 GATTTGTTGTTAAAATATCACATACAAAACTCCCACCGGATGGTCAGACACCCAAGGAAATAAGA
1 GATTTGTTGTTAAAATATCACATACAAAACTCCCACCGGATGGTCAGACACCCAAGGAAATAAGA
46996 CAATCGGGACTTGTCGACATAGTTTTTTTTTTTTTTGGGTGAACAAGGGAAACAAACCAGATTAG
66 CAATCGGGACTTGTCGACATAGTTTTTTTTTTTTTTGGGTGAACAAGGGAAACAAACCAGATTAG
47061 CAATTACAAAACATGGATTTCAGTCA
131 CAATTACAAAACATGGATTTCAGTCA
47087 ACTCGTCCTG
Statistics
Matches: 156, Mismatches: 0, Indels: 4
0.98 0.00 0.03
Matches are distributed among these distances:
156 69 0.44
160 87 0.56
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (156 bp):
GATTTGTTGTTAAAATATCACATACAAAACTCCCACCGGATGGTCAGACACCCAAGGAAATAAGA
CAATCGGGACTTGTCGACATAGTTTTTTTTTTTTTTGGGTGAACAAGGGAAACAAACCAGATTAG
CAATTACAAAACATGGATTTCAGTCA
Found at i:50713 original size:15 final size:15
Alignment explanation
Indices: 50689--50718 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
50679 TAATTAAAGT
*
50689 TTAGTTTCTATTTTA
1 TTAGTATCTATTTTA
50704 TTAGTATCTATTTTA
1 TTAGTATCTATTTTA
50719 AAATTTAACG
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:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (15 bp):
TTAGTATCTATTTTA
Found at i:55153 original size:27 final size:27
Alignment explanation
Indices: 55123--55264 Score: 284
Period size: 27 Copynumber: 5.3 Consensus size: 27
55113 AGGTTTCATA
55123 GAACTATTCACGATAGTGAAATAGTGT
1 GAACTATTCACGATAGTGAAATAGTGT
55150 GAACTATTCACGATAGTGAAATAGTGT
1 GAACTATTCACGATAGTGAAATAGTGT
55177 GAACTATTCACGATAGTGAAATAGTGT
1 GAACTATTCACGATAGTGAAATAGTGT
55204 GAACTATTCACGATAGTGAAATAGTGT
1 GAACTATTCACGATAGTGAAATAGTGT
55231 GAACTATTCACGATAGTGAAATAGTGT
1 GAACTATTCACGATAGTGAAATAGTGT
55258 GAACTAT
1 GAACTAT
55265 CCGTAAAAGA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (27 bp):
GAACTATTCACGATAGTGAAATAGTGT
Found at i:56177 original size:31 final size:31
Alignment explanation
Indices: 56139--56295 Score: 226
Period size: 31 Copynumber: 5.0 Consensus size: 31
56129 TCCGAAGGAC
* * *
56139 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
56170 CAGTCCATATGTCCCGAAGGACATAGGTAAAA
1 CAGTCCATATGTCCCGAAGAACATAGGT-AAA
* * *
56202 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
56233 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
56264 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
56295 C
1 C
56296 CCTCGACCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
31 85 0.75
32 28 0.25
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:56238 original size:63 final size:62
Alignment explanation
Indices: 56139--56293 Score: 249
Period size: 63 Copynumber: 2.5 Consensus size: 62
56129 TCCGAAGGAC
* *
56139 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGT-AAA
*
56202 CAGTCCGTATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
56264 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
56294 ACCCTCGACC
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
62 31 0.36
63 54 0.63
64 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:56497 original size:23 final size:22
Alignment explanation
Indices: 56471--56515 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
56461 ATATACTTGT
*
56471 TTTCACATATATATTTCATATCA
1 TTTCACATACA-ATTTCATATCA
*
56494 TTTCACATACACTTTCATATCA
1 TTTCACATACAATTTCATATCA
56516 CATGCCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTCACATACAATTTCATATCA
Found at i:57184 original size:20 final size:21
Alignment explanation
Indices: 57145--57188 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
57135 ATTCTGTCGT
*
57145 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCCGTTCCCC
*
57166 TTGAATGGGTA-CCGTTCCCC
1 TTGAAGGGGTATCCGTTCCCC
57186 TTG
1 TTG
57189 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.14, C:0.25, G:0.30, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTATCCGTTCCCC
Found at i:59780 original size:31 final size:31
Alignment explanation
Indices: 59742--59897 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
59732 CCCGAAGGAC
* * *
59742 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
59773 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* * *
59804 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59835 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59866 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59897 C
1 C
59898 CCTCGACCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:60101 original size:23 final size:24
Alignment explanation
Indices: 60075--60121 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
60065 ATATACTTGT
*
60075 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
60098 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
60122 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:60780 original size:21 final size:21
Alignment explanation
Indices: 60750--60794 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
60740 ATTCTGTCGT
* *
60750 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
60771 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
60792 TTG
1 TTG
60795 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:78453 original size:2 final size:2
Alignment explanation
Indices: 78446--78510 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
78436 ATCATTCCCC
78446 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
78488 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
78511 AATCTTCTAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.