Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001788.1 Hibiscus syriacus cultivar Beakdansim tig00003608_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: 56766
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3995 original size:2 final size:2
Alignment explanation
Indices: 3988--4078 Score: 148
Period size: 2 Copynumber: 45.0 Consensus size: 2
3978 ACATTTCATA
*
3988 AT AT AT AT AT AT AT AT AT AT AT -T AT GAGG AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT
4031 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
4073 AT AT AT
1 AT AT AT
4079 GAGGAACATA
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 1 0.01
2 81 0.96
3 2 0.02
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4689 original size:22 final size:22
Alignment explanation
Indices: 4671--4719 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
4661 TATTCCACAT
*
4671 GTATTGAGTGTTAAATCCACTA
1 GTATTAAGTGTTAAATCCACTA
4693 GTATTAAGTGTTAAATCCACTA
1 GTATTAAGTGTTAAATCCACTA
*
4715 ATATT
1 GTATT
4720 GAATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
GTATTAAGTGTTAAATCCACTA
Found at i:4728 original size:22 final size:22
Alignment explanation
Indices: 4672--4728 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4662 ATTCCACATG
* *
4672 TATTGAGTGTTAAATCCACTAG
1 TATTGAATGTTAAATCCACTAA
4694 TATT-AAGTGTTAAATCCACTAA
1 TATTGAA-TGTTAAATCCACTAA
*
4716 TATTGAATATTAA
1 TATTGAATGTTAA
4729 TTTTATGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 27 0.90
23 2 0.07
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (22 bp):
TATTGAATGTTAAATCCACTAA
Found at i:9294 original size:31 final size:31
Alignment explanation
Indices: 9259--9318 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
9249 TCAAACCCAA
9259 GAGTTCCTAGTGAGAA-AGACATATTGAATGG
1 GAGTTCCTAGTGAGAAGA-ACATATTGAATGG
9290 GAGTTCCTAGTGAGAAGAACATATTGAAT
1 GAGTTCCTAGTGAGAAGAACATATTGAAT
9319 TCACCGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (31 bp):
GAGTTCCTAGTGAGAAGAACATATTGAATGG
Found at i:9927 original size:22 final size:22
Alignment explanation
Indices: 9902--9978 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
9892 GTTAGGTTAT
*
9902 TCCACTAGTATTGAGTGTTAAA
1 TCCACTAGTATTAAGTGTTAAA
* *
9924 TCCACTAATATTAAGTGATAAA
1 TCCACTAGTATTAAGTGTTAAA
9946 TCCACTAGTATTAAGTGTTAAA
1 TCCACTAGTATTAAGTGTTAAA
9968 TCC-CTAGTATT
1 TCCACTAGTATT
9979 GAATATTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 8 0.16
22 42 0.84
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
TCCACTAGTATTAAGTGTTAAA
Found at i:10931 original size:78 final size:78
Alignment explanation
Indices: 10839--10994 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
10829 TAATTTTTCA
10839 GCAAGCAGTTTTTTCGAACAGAACTTAAGTTCTCTCTTCATTTGAATTCTCACTTCCTTTAATTA
1 GCAAGCAGTTTTTTCGAACAGAACTTAAGTTCTCTCTTCATTTGAATTCTCACTTCCTTTAATTA
10904 CAATCAATAATGT
66 CAATCAATAATGT
* *
10917 GCAAGCAGTTTTTTCGAACAGAACTTATGTTCTCTCTTCATTTGAATTCTCACTTCGTTTAATTA
1 GCAAGCAGTTTTTTCGAACAGAACTTAAGTTCTCTCTTCATTTGAATTCTCACTTCCTTTAATTA
10982 CAATCAATAATGT
66 CAATCAATAATGT
10995 ATGTGATGTA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (78 bp):
GCAAGCAGTTTTTTCGAACAGAACTTAAGTTCTCTCTTCATTTGAATTCTCACTTCCTTTAATTA
CAATCAATAATGT
Found at i:16910 original size:2 final size:2
Alignment explanation
Indices: 16899--16942 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
16889 GAGGATACTC
*
16899 AT AT AC 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
16941 AT
1 AT
16943 TCTGTATACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21717 original size:21 final size:21
Alignment explanation
Indices: 21691--21730 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21681 AGACAATTTG
* *
21691 TACTCCACAGCAGGTGGAGCA
1 TACTCCAAAACAGGTGGAGCA
21712 TACTCCAAAACAGGTGGAG
1 TACTCCAAAACAGGTGGAG
21731 TTTTAGCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.15
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGCA
Found at i:27798 original size:9 final size:9
Alignment explanation
Indices: 27784--27868 Score: 53
Period size: 10 Copynumber: 8.8 Consensus size: 9
27774 GGCTGCTGGA
27784 AACCGGTTT
1 AACCGGTTT
27793 AACCGGTTTT
1 AACCGG-TTT
*
27803 CAACCGATTCT
1 -AACCGGTT-T
*
27814 GACCGGTTT
1 AACCGGTTT
*
27823 CAACCGGTTCG
1 -AACCGGTT-T
*
27834 CACCGGTTT
1 AACCGGTTT
* *
27843 GACCGGTCTG
1 AACCGGT-TT
27853 AACCGGTTT
1 AACCGGTTT
*
27862 GACCGGT
1 AACCGGT
27869 CTGACCCGAC
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
9 20 0.34
10 32 0.55
11 6 0.10
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:27823 original size:20 final size:20
Alignment explanation
Indices: 27794--27842 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
27784 AACCGGTTTA
27794 ACCGGTTTTCAACCGATTCTG-
1 ACCGG-TTTCAACCGATTC-GC
*
27815 ACCGGTTTCAACCGGTTCGC
1 ACCGGTTTCAACCGATTCGC
27835 ACCGGTTT
1 ACCGGTTT
27843 GACCGGTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (20 bp):
ACCGGTTTCAACCGATTCGC
Found at i:27849 original size:19 final size:20
Alignment explanation
Indices: 27805--27872 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
27795 CCGGTTTTCA
* *
27805 ACCGATTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
*
27825 ACCGGTTC-GCACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
27844 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
27863 ACCGG-TCTGA
1 ACCGGTTCTGA
27873 CCCGACCCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.05
19 26 0.60
20 15 0.35
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.26
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:27873 original size:9 final size:9
Alignment explanation
Indices: 27835--27874 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
27825 ACCGGTTCGC
*
27835 ACCGGTTTG
1 ACCGGTCTG
27844 ACCGGTCTG
1 ACCGGTCTG
*
27853 AACCGGTTTG
1 -ACCGGTCTG
27863 ACCGGTCTG
1 ACCGGTCTG
27872 ACC
1 ACC
27875 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:27898 original size:17 final size:17
Alignment explanation
Indices: 27876--27913 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
27866 GGTCTGACCC
27876 GACCCGACCCGACCATT
1 GACCCGACCCGACCATT
*
27893 GACCCGACCCGACCGTT
1 GACCCGACCCGACCATT
27910 GACC
1 GACC
27914 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCATT
Found at i:30445 original size:35 final size:35
Alignment explanation
Indices: 30395--30488 Score: 143
Period size: 35 Copynumber: 2.7 Consensus size: 35
30385 AGAATACAAG
* * * *
30395 TAACATAGTTAAAAATATAATTATTTGGATACGAA
1 TAACATAGCTCAAAATATAATTATCTAGATACGAA
30430 TAACATAGCTCAAAATATAATTATCTAGATACGAA
1 TAACATAGCTCAAAATATAATTATCTAGATACGAA
*
30465 TAACATAGCTCAAAATGTAATTAT
1 TAACATAGCTCAAAATATAATTAT
30489 ATCTAGTTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.32
Consensus pattern (35 bp):
TAACATAGCTCAAAATATAATTATCTAGATACGAA
Found at i:36443 original size:29 final size:29
Alignment explanation
Indices: 36410--36479 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
36400 TTTCTTGGGT
36410 TCTGAGTTTGC-TATGAAGGACTTAGGTCC
1 TCTGAGTTT-CTTATGAAGGACTTAGGTCC
36439 TCTGAGTTTCTTATGAAGGACTTAGGTCC
1 TCTGAGTTTCTTATGAAGGACTTAGGTCC
36468 TCTGAGTTTCTT
1 TCTGAGTTTCTT
36480 TTTGGGTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (29 bp):
TCTGAGTTTCTTATGAAGGACTTAGGTCC
Found at i:38942 original size:61 final size:61
Alignment explanation
Indices: 38847--38962 Score: 214
Period size: 61 Copynumber: 1.9 Consensus size: 61
38837 CTGTTGAAGG
*
38847 TTGGATCTTGAGCGGTAACAACCCATCTCCAACGCCCGTGGATCACCGGCAACAACCCGTT
1 TTGGATCTTGAGCGGTAACAACCCATCCCCAACGCCCGTGGATCACCGGCAACAACCCGTT
*
38908 TTGGATCTTGAGCGGTAACAACCCATCCCCAACGCCCGTGGTTCACCGGCAACAA
1 TTGGATCTTGAGCGGTAACAACCCATCCCCAACGCCCGTGGATCACCGGCAACAA
38963 TCAGCGCCCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (61 bp):
TTGGATCTTGAGCGGTAACAACCCATCCCCAACGCCCGTGGATCACCGGCAACAACCCGTT
Found at i:39351 original size:34 final size:34
Alignment explanation
Indices: 39308--39373 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
39298 TTTATACACC
39308 CTTAGCATCACCCTCTAATTGTAGCTATTTGCAT
1 CTTAGCATCACCCTCTAATTGTAGCTATTTGCAT
39342 CTTAGCATCACCCTCTAATTGTAGCTATTTGC
1 CTTAGCATCACCCTCTAATTGTAGCTATTTGC
39374 TGATGTTCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (34 bp):
CTTAGCATCACCCTCTAATTGTAGCTATTTGCAT
Found at i:39462 original size:16 final size:16
Alignment explanation
Indices: 39437--39467 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39427 AAATTTGTGG
39437 TTTTAAAAAAATATAA
1 TTTTAAAAAAATATAA
*
39453 TTTTAGAAAAATATA
1 TTTTAAAAAAATATA
39468 CTTTCTCTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTTAAAAAAATATAA
Found at i:47565 original size:16 final size:16
Alignment explanation
Indices: 47544--47579 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
47534 AACCATCTAA
* *
47544 TTAAGAGTATTTTAGT
1 TTAAGAGAATTTTAAT
47560 TTAAGAGAATTTTAAT
1 TTAAGAGAATTTTAAT
47576 TTAA
1 TTAA
47580 TTATTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (16 bp):
TTAAGAGAATTTTAAT
Found at i:51992 original size:59 final size:59
Alignment explanation
Indices: 51918--52046 Score: 143
Period size: 60 Copynumber: 2.2 Consensus size: 59
51908 AGTTGGGTTT
* * * ** * * *
51918 TTAAACTTTTGAATATTCCAGCTTCAT-TTCAAATTATTATTCTCATTTTAAATTAATTC
1 TTAAACTTTTAAATATTCAAACTTCATCCCCAAATTATAATTCTCATTCTAAATT-AGTC
* *
51977 TTAAACTTTTAAATATTTAAATTTCATCCCCAAATTATAATTCTCATTCTAAATTAGTC
1 TTAAACTTTTAAATATTCAAACTTCATCCCCAAATTATAATTCTCATTCTAAATTAGTC
52036 TCTAAACTTTT
1 T-TAAACTTTT
52047 GAGCATTTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 26 0.45
60 32 0.55
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.47
Consensus pattern (59 bp):
TTAAACTTTTAAATATTCAAACTTCATCCCCAAATTATAATTCTCATTCTAAATTAGTC
Found at i:52030 original size:60 final size:60
Alignment explanation
Indices: 51947--52064 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
51937 AGCTTCATTT
* * * *
51947 CAAATTATTATTCTCATTTTAAATTAAT-TCTTAAACTTTTAAATATTTAAATTTCATCCC
1 CAAATTATAATTCTCATTCTAAATTAGTCTC-TAAACTTTTAAACATTTAAATTTCATCCC
* * *
52007 CAAATTATAATTCTCATTCTAAATTAGTCTCTAAACTTTTGAGCATTTGAATTTCATC
1 CAAATTATAATTCTCATTCTAAATTAGTCTCTAAACTTTTAAACATTTAAATTTCATC
52065 TCAAACGATC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 48 0.96
61 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.03, T:0.46
Consensus pattern (60 bp):
CAAATTATAATTCTCATTCTAAATTAGTCTCTAAACTTTTAAACATTTAAATTTCATCCC
Found at i:53879 original size:16 final size:16
Alignment explanation
Indices: 53860--53901 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
53850 ACCAAAGATG
53860 TCAAATTTGCCAACTT
1 TCAAATTTGCCAACTT
*
53876 TCAATTTTGCCAACTT
1 TCAAATTTGCCAACTT
*
53892 TCAACTTTGC
1 TCAAATTTGC
53902 TAATTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.40
Consensus pattern (16 bp):
TCAAATTTGCCAACTT
Done.