Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007258.1 Hibiscus syriacus cultivar Beakdansim tig00019238_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: 58473
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:673 original size:9 final size:9
Alignment explanation
Indices: 661--685 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
651 GTAAAAAATG
661 AATAAAACA
1 AATAAAACA
670 AATAAAACA
1 AATAAAACA
679 AATAAAA
1 AATAAAA
686 TGAAGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
AATAAAACA
Found at i:984 original size:2 final size:2
Alignment explanation
Indices: 977--1054 Score: 69
Period size: 2 Copynumber: 41.5 Consensus size: 2
967 TATACGTATG
*
977 TA TA TA TA TA TA TA TA -A TGA AA TA TA -A TA -A TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
* * *
1015 AA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1055 TAACATACTG
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
1 6 0.10
2 55 0.89
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2820 original size:99 final size:99
Alignment explanation
Indices: 2698--2882 Score: 289
Period size: 99 Copynumber: 1.9 Consensus size: 99
2688 CTGAAACTGA
* *
2698 AAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTCGAGTAT
1 AAAGTTGTTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTCGAGTAC
*
2763 AATATCCTTCGTTGCGAAGTTGAGATTGACTCTG
66 AATATCCTTCGCTGCGAAGTTGAGATTGACTCTG
* * * * *
2797 AAAGTTGTTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCC
1 AAAGTTGTTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTCGAGTAC
*
2862 AATATCCTTCGCTGTGAAGTT
66 AATATCCTTCGCTGCGAAGTT
2883 AAAATTGGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 77 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (99 bp):
AAAGTTGTTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTCGAGTAC
AATATCCTTCGCTGCGAAGTTGAGATTGACTCTG
Found at i:12847 original size:18 final size:18
Alignment explanation
Indices: 12773--12848 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 18
12763 TGAAAGTAAT
12773 ATAAAATGAAG-AAGATAA
1 ATAAAATGAAGAAAGAT-A
* * *
12791 AAAAAATAAAGTAAAGGTA
1 ATAAAATGAAG-AAAGATA
* *
12810 A-AAAATGAATAAA-ACAA
1 ATAAAATGAAGAAAGA-TA
12827 ATAAAATGAAGAAAGATA
1 ATAAAATGAAGAAAGATA
12845 ATAA
1 ATAA
12849 TAATAATAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
17 5 0.11
18 32 0.73
19 3 0.07
20 4 0.09
ACGTcount: A:0.70, C:0.01, G:0.13, T:0.16
Consensus pattern (18 bp):
ATAAAATGAAGAAAGATA
Found at i:13131 original size:2 final size:2
Alignment explanation
Indices: 13118--13212 Score: 110
Period size: 2 Copynumber: 49.5 Consensus size: 2
13108 ATACTAAGCG
* *
13118 TA TA TG TA TA TA TA TA TA TA TA TA TA TA -A TGA AA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
*
13159 -A TA -A TA -A TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
13198 TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA T
13213 TAACATACTG
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
1 5 0.06
2 73 0.92
3 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:33573 original size:5 final size:5
Alignment explanation
Indices: 33563--33588 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33553 TTAATGTTTC
33563 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
33589 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:37503 original size:16 final size:16
Alignment explanation
Indices: 37482--37512 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
37472 CTTTAGGTCT
37482 GTTTTAGTTTTAGTCC
1 GTTTTAGTTTTAGTCC
37498 GTTTTAGTTTTAGTC
1 GTTTTAGTTTTAGTC
37513 AGTTCTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.58
Consensus pattern (16 bp):
GTTTTAGTTTTAGTCC
Found at i:42456 original size:14 final size:14
Alignment explanation
Indices: 42437--42476 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
42427 AATGGGAAGT
42437 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
42451 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
42465 AATCTCTGCATA
1 AATCCCTGCATA
42477 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:57797 original size:23 final size:23
Alignment explanation
Indices: 57771--57827 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
57761 AAGGTTTTTA
* * *
57771 AATAGATTTTTTATTTTATTAAT
1 AATAAATTTTATACTTTATTAAT
57794 AATAAATTTTATACTTTATTAAT
1 AATAAATTTTATACTTTATTAAT
57817 AATAAATTTTA
1 AATAAATTTTA
57828 AATACCAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
AATAAATTTTATACTTTATTAAT
Done.