Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001031.1 Hibiscus syriacus cultivar Beakdansim tig00002053_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: 73843
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1769 original size:162 final size:158
Alignment explanation
Indices: 1502--1822 Score: 597
Period size: 162 Copynumber: 2.0 Consensus size: 158
1492 TGCAAGGCGT
*
1502 ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGGCACAAAAAAGCTCTAGCCTGAGTA
1 ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGACACAAAAAAGCTCTAGCCTGAGTA
1567 AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCCGGGG
66 AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCC--GG
1632 TGGGGGGAGGTTTATGCCTACCGCCTTAGAGA
129 -GGGGGGAGGTTTATGCCTA-CGCCTTAGAGA
1664 ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGACACAAAAAAGCTCTAGCCTGAGTA
1 ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGACACAAAAAAGCTCTAGCCTGAGTA
1729 AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCCGGGG
66 AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCCGGGG
1794 GGGGAGGTTTATGCCTACGCCTTAGAGA
131 GGGGAGGTTTATGCCTACGCCTTAGAGA
1822 A
1 A
1823 AAGTGTGCCT
Statistics
Matches: 158, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
158 12 0.08
159 19 0.12
160 2 0.01
162 125 0.79
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (158 bp):
ACTCTAGGTGCTTCAACCCGTACATTGCCTCAGGCGCTCGACACAAAAAAGCTCTAGCCTGAGTA
AAGCATAGAAAATGAAAGAAAAAAGGTGAACAATGAAAGAAACTAAAAATAAATTTAATCCGGGG
GGGGAGGTTTATGCCTACGCCTTAGAGA
Found at i:9568 original size:29 final size:29
Alignment explanation
Indices: 9531--9596 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
9521 TTGAGTCTCT
9531 CGACTATTAAAAGTTACAAAATGGTTATC
1 CGACTATTAAAAGTTACAAAATGGTTATC
9560 CGACTATTAAAAGTTACAAAATGGTTATC
1 CGACTATTAAAAGTTACAAAATGGTTATC
9589 CGACTATT
1 CGACTATT
9597 CATTATGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (29 bp):
CGACTATTAAAAGTTACAAAATGGTTATC
Found at i:17565 original size:34 final size:34
Alignment explanation
Indices: 17459--17557 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 34
17449 ATAAATGTTT
* *
17459 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
17493 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
17527 TTAAAATATAAATTATAGTATTCGAAATTTA
1 TTAAAATAAAAATTATATTATTCGAAATTTA
17558 TCATTAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:18277 original size:8 final size:8
Alignment explanation
Indices: 18264--18304 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
18254 TCACAAGCTT
18264 TCAAATTC
1 TCAAATTC
18272 TCAAATTC
1 TCAAATTC
* *
18280 CCAAACTC
1 TCAAATTC
18288 T-AAATTC
1 TCAAATTC
18295 TCAAATTC
1 TCAAATTC
18303 TC
1 TC
18305 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:23558 original size:2 final size:2
Alignment explanation
Indices: 23551--23589 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
23541 TCAAGCTTTC
23551 AT AT AT AT AT AT AT AT AT AT AT AT 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
23590 CCACTTGCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24061 original size:2 final size:2
Alignment explanation
Indices: 24054--24101 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
24044 TCATTATCAA
24054 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
24096 AT AT AT
1 AT AT AT
24102 CTCGTCATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25883 original size:27 final size:26
Alignment explanation
Indices: 25843--25905 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 26
25833 GACCTTGTCA
*
25843 CTTTCGGCTCCAAAAACTCTTTCCCTG
1 CTTTC-GCTTCAAAAACTCTTTCCCTG
25870 CTTTCTGCTTCAAAAACTCTTTCCCTG
1 CTTTC-GCTTCAAAAACTCTTTCCCTG
25897 CTTTCGCTT
1 CTTTCGCTT
25906 TCTTCGGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 4 0.12
27 30 0.88
ACGTcount: A:0.16, C:0.35, G:0.10, T:0.40
Consensus pattern (26 bp):
CTTTCGCTTCAAAAACTCTTTCCCTG
Found at i:32313 original size:26 final size:26
Alignment explanation
Indices: 32284--32335 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
32274 GTGAAATAAC
*
32284 TTAAGAAATTACAATTTTAGAATGTT
1 TTAAGAAATTAAAATTTTAGAATGTT
32310 TTAAGAAATTAAAATTTTAGAATGTT
1 TTAAGAAATTAAAATTTTAGAATGTT
32336 ATAGTGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (26 bp):
TTAAGAAATTAAAATTTTAGAATGTT
Found at i:47505 original size:2 final size:2
Alignment explanation
Indices: 47500--47524 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47490 ATTTTAAACT
47500 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
47525 GTATGAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59801 original size:28 final size:29
Alignment explanation
Indices: 59778--59836 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
59768 TTATAATTCA
59778 AATA-TTT-AAAAATACTAAAAATAAATT
1 AATATTTTAAAAAATACTAAAAATAAATT
* *
59805 ACTATTTTAAAAAATACTAAAAACAATATT
1 AATATTTTAAAAAATACTAAAAATAA-ATT
59835 AA
1 AA
59837 AAATAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 3 0.12
28 3 0.12
29 16 0.62
30 4 0.15
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (29 bp):
AATATTTTAAAAAATACTAAAAATAAATT
Found at i:59875 original size:29 final size:30
Alignment explanation
Indices: 59812--59875 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
59802 ATTACTATTT
*
59812 TAAAAAATACTAAAAACAATATTAAAAATA
1 TAAAAAATAATAAAAACAATATTAAAAATA
*
59842 -AAAAAAAAATAAAAAC-ATA-TAACAAACTA
1 TAAAAAATAATAAAAACAATATTAA-AAA-TA
59871 TAAAA
1 TAAAA
59876 TGATCAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 3 0.10
28 6 0.21
29 16 0.55
30 4 0.14
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (30 bp):
TAAAAAATAATAAAAACAATATTAAAAATA
Found at i:71305 original size:7 final size:7
Alignment explanation
Indices: 71295--71395 Score: 76
Period size: 7 Copynumber: 14.4 Consensus size: 7
71285 TATTGGATTA
71295 AGGGTTT
1 AGGGTTT
71302 AGGGTTT
1 AGGGTTT
71309 AGGGTTT
1 AGGGTTT
** *
71316 ATAGATT
1 AGGGTTT
* *
71323 ATGGATT
1 AGGGTTT
*
71330 AAGGTTT
1 AGGGTTT
*
71337 AGTGTTT
1 AGGGTTT
*
71344 AGGTTTT
1 AGGGTTT
* *
71351 AAGATTT
1 AGGGTTT
*
71358 AAGGTTT
1 AGGGTTT
71365 AGGGTTT
1 AGGGTTT
71372 AGGGTTT
1 AGGGTTT
**
71379 AGAATTT
1 AGGGTTT
*
71386 AGGATTT
1 AGGGTTT
71393 AGG
1 AGG
71396 TTAAGGTATA
Statistics
Matches: 77, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 77 1.00
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.44
Consensus pattern (7 bp):
AGGGTTT
Found at i:71385 original size:28 final size:28
Alignment explanation
Indices: 71328--71395 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
71318 AGATTATGGA
* *
71328 TTAAGGTTTAGTGTTTAGGTTTTAAGAT
1 TTAAGGTTTAGGGTTTAGGGTTTAAGAT
71356 TTAAGGTTTAGGGTTTAGGGTTT-AGAAT
1 TTAAGGTTTAGGGTTTAGGGTTTAAG-AT
71384 TT-AGGATTTAGG
1 TTAAGG-TTTAGG
71396 TTAAGGTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 5 0.14
28 31 0.86
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (28 bp):
TTAAGGTTTAGGGTTTAGGGTTTAAGAT
Done.