Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005347.1 Hibiscus syriacus cultivar Beakdansim tig00012124_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: 38381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:827 original size:28 final size:28
Alignment explanation
Indices: 774--827 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
764 AAAATAGTTC
* *
774 AATGACTAAAATGTAAATTAATAATATA
1 AATGACCAAAATGTAAATAAATAATATA
*
802 AATGACCAAAAT-TTAATAAATCAATA
1 AATGACCAAAATGTAAATAAAT-AATA
828 ACGTAAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.30
Consensus pattern (28 bp):
AATGACCAAAATGTAAATAAATAATATA
Found at i:932 original size:13 final size:13
Alignment explanation
Indices: 914--938 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
904 TTTTTTTAAT
914 TTTTCCTATTTTG
1 TTTTCCTATTTTG
927 TTTTCCTATTTT
1 TTTTCCTATTTT
939 AATAGTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTCCTATTTTG
Found at i:4739 original size:14 final size:15
Alignment explanation
Indices: 4709--4742 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
4699 TGGACCGTCT
4709 CTAATATATTAAATG
1 CTAATATATTAAATG
4724 CTAATATATT-AATG
1 CTAATATATTAAATG
4738 CTAAT
1 CTAAT
4743 TTACCAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (15 bp):
CTAATATATTAAATG
Found at i:8182 original size:13 final size:13
Alignment explanation
Indices: 8164--8197 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
8154 TAGCATATTA
*
8164 GCCTTCGTTTGTT
1 GCCTTCATTTGTT
8177 GCCTTCATTTGTT
1 GCCTTCATTTGTT
*
8190 GCTTTCAT
1 GCCTTCAT
8198 GTGGTTCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.53
Consensus pattern (13 bp):
GCCTTCATTTGTT
Found at i:15891 original size:6 final size:6
Alignment explanation
Indices: 15868--15905 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
15858 TTTAATAAGT
*
15868 AATAAA TATAAA AGATAAA AAT-AA AATAAA AATAAA AA
1 AATAAA AATAAA A-ATAAA AATAAA AATAAA AATAAA AA
15906 CCTGAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:16795 original size:23 final size:23
Alignment explanation
Indices: 16731--16796 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
16721 GTTCGTTTGT
* *
16731 TTAATATTCACAAACACATTTAT
1 TTAATATTCACAAACATATTTAA
* * *
16754 TTAACATTCGCAAAAATATTTAA
1 TTAATATTCACAAACATATTTAA
16777 TTAATATTCACAAACATATT
1 TTAATATTCACAAACATATT
16797 CACTTTATGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (23 bp):
TTAATATTCACAAACATATTTAA
Found at i:18577 original size:19 final size:19
Alignment explanation
Indices: 18555--18613 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
18545 TGTATGTATG
18555 TATGTATGTATATATAATT
1 TATGTATGTATATATAATT
* * *
18574 TATGTATGTCTATTTTATT
1 TATGTATGTATATATAATT
* * *
18593 AATGCATGCAT-TATAATT
1 TATGTATGTATATATAATT
18611 TAT
1 TAT
18614 TATTGCATGT
Statistics
Matches: 30, Mismatches: 10, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (19 bp):
TATGTATGTATATATAATT
Found at i:18577 original size:23 final size:23
Alignment explanation
Indices: 18516--18582 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
18506 AATAAATTAA
18516 ACTATGATATGTATGTATGATATGT
1 ACTAT-ATATGTATGTATG-TATGT
*
18541 ACTATGTATGTATGTATGTATGT
1 ACTATATATGTATGTATGTATGT
*
18564 A-TATATAATTTATGTATGT
1 ACTATAT-ATGTATGTATGT
18583 CTATTTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 4 0.11
23 17 0.45
24 12 0.32
25 5 0.13
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.48
Consensus pattern (23 bp):
ACTATATATGTATGTATGTATGT
Found at i:18582 original size:4 final size:4
Alignment explanation
Indices: 18518--18565 Score: 62
Period size: 4 Copynumber: 11.8 Consensus size: 4
18508 TAAATTAAAC
*
18518 TATG ATATG TATG TATG ATATG TA-C TATG TATG TATG TATG TATG TAT
1 TATG -TATG TATG TATG -TATG TATG TATG TATG TATG TATG TATG TAT
18566 ATATAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
3 2 0.05
4 29 0.74
5 8 0.21
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:18800 original size:28 final size:28
Alignment explanation
Indices: 18768--18822 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
18758 TTTATAATTT
18768 ACTTCAAACCATATAAATTAAATCATAA
1 ACTTCAAACCATATAAATTAAATCATAA
** *
18796 ACTTCAAACGTTATAAATTATATCATA
1 ACTTCAAACCATATAAATTAAATCATA
18823 CATTCATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (28 bp):
ACTTCAAACCATATAAATTAAATCATAA
Found at i:25845 original size:181 final size:173
Alignment explanation
Indices: 25496--25852 Score: 561
Period size: 181 Copynumber: 2.0 Consensus size: 173
25486 TCTTCGGGTG
*
25496 AGCCTAGTGGAGTAAGTCTAGACCTTGAATATTCAGTTCGTTGATCAGATAGTTTTTGGCAAAAG
1 AGCCTAGTGGAATAAGTCTAGACCTTGAATATTCAGTTCGTTGATCAGATAGTTTTTGGCAAAAG
* *
25561 ATCCGACTTGGAAGCCTATTGGTTCAATACTACTAATCAAAGAATCAATTCCTTTGATCGGTGAT
66 ATCCGACTTGGAAGCCTATTGGTTCAATACTACAAATCAAAGAATCAATTCCTTTGATCAGTGAT
25626 GATAACTGTCGCACAGTGAGGATCGATGTCAGGCTTGCAGTGT
131 GATAACTGTCGCACAGTGAGGATCGATGTCAGGCTTGCAGTGT
*
25669 AGCCTAGTGGAATAAGTTTAGACCTTGGAATATTCAGTTCGTTGATCAGATAGTTTTTGGCAAAA
1 AGCCTAGTGGAATAAGTCTAGACCTT-GAATATTCAGTTCGTTGATCAGATAGTTTTTGGCAAAA
* * *
25734 GATCTGACTTGGAAGCCTATTGGTTTAGTACTACAAAATACAAATCAAAGAATCGATTCCTTTGA
65 GATCCGACTTGGAAGCCTATTGGTTCA--A-TAC----TACAAATCAAAGAATCAATTCCTTTGA
* *
25799 TCAGTGATGATAACTGTTGCACGGTGAGGATCGATGTCAGGCTTGCAGTGT
123 TCAGTGATGATAACTGTCGCACAGTGAGGATCGATGTCAGGCTTGCAGTGT
25850 AGC
1 AGC
25853 TTGAATTGAT
Statistics
Matches: 167, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
173 24 0.14
174 63 0.38
176 1 0.01
177 3 0.02
181 76 0.46
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (173 bp):
AGCCTAGTGGAATAAGTCTAGACCTTGAATATTCAGTTCGTTGATCAGATAGTTTTTGGCAAAAG
ATCCGACTTGGAAGCCTATTGGTTCAATACTACAAATCAAAGAATCAATTCCTTTGATCAGTGAT
GATAACTGTCGCACAGTGAGGATCGATGTCAGGCTTGCAGTGT
Found at i:35492 original size:2 final size:2
Alignment explanation
Indices: 35485--35563 Score: 135
Period size: 2 Copynumber: 40.5 Consensus size: 2
35475 AATGGGAATC
*
35485 AT AT AT AT AT AT AT AT AT AT AT CT 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
35527 AT AT AT -T AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35564 AGAATAATAG
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 71 0.97
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.