Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002246.1 Hibiscus syriacus cultivar Beakdansim tig00004564_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: 58649
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:473 original size:2 final size:2
Alignment explanation
Indices: 466--494 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
456 TTGCTTGTTT
466 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
495 AAAGTTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1187 original size:21 final size:21
Alignment explanation
Indices: 1149--1204 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1139 TTCATGTTCG
*
1149 ATTCATTTAACATCCACAAAC
1 ATTCATTTAATATCCACAAAC
* *
1170 ATTCATTTAATGTTCACAAAC
1 ATTCATTTAATATCCACAAAC
*
1191 ATGTTATTTAATAT
1 AT-TCATTTAATAT
1205 TGACGAACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTCATTTAATATCCACAAAC
Found at i:1213 original size:22 final size:23
Alignment explanation
Indices: 1150--1223 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
1140 TCATGTTCGA
* *
1150 TTCATTTAACATCCACAAAC-A-
1 TTCATTTAATATTCACAAACAAG
* *
1171 TTCATTTAATGTTCACAAACATG
1 TTCATTTAATATTCACAAACAAG
* *
1194 TT-ATTTAATATTGACGAACAAG
1 TTCATTTAATATTCACAAACAAG
1216 TTCATTTA
1 TTCATTTA
1224 TATGGTTGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.40
22 18 0.43
23 7 0.17
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (23 bp):
TTCATTTAATATTCACAAACAAG
Found at i:8850 original size:29 final size:29
Alignment explanation
Indices: 8817--8872 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
8807 TCCCAACACA
*
8817 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
8846 TAGGTCGTCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
8873 ACCCTCGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:8925 original size:33 final size:33
Alignment explanation
Indices: 8888--8960 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
8878 CGCACGGCTT
* *
8888 CCCTCGGATTCCCTCACATAGCTCGCTCGGTTG
1 CCCTCGGATGCCCTCACATAGCTCGCTCGGATG
* *
8921 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
1 CCCTCGGATGCCCTCACATAGCTCGCTCGGATG
*
8954 GCCTCGG
1 CCCTCGG
8961 TCGGATGGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.38, G:0.26, T:0.25
Consensus pattern (33 bp):
CCCTCGGATGCCCTCACATAGCTCGCTCGGATG
Found at i:8964 original size:14 final size:14
Alignment explanation
Indices: 8942--9012 Score: 96
Period size: 14 Copynumber: 5.4 Consensus size: 14
8932 CCTCGCATAG
*
8942 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
8956 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
8970 CTCGGTCGGATGG-
1 CTCGGTCGGATGGC
8983 C-C--TCGGATGGC
1 CTCGGTCGGATGGC
*
8994 CTCGGTCGGATGGT
1 CTCGGTCGGATGGC
9008 CTCGG
1 CTCGG
9013 ATGCCCAGCG
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
10 8 0.16
11 1 0.02
12 2 0.04
13 1 0.02
14 39 0.76
ACGTcount: A:0.07, C:0.28, G:0.41, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:8988 original size:24 final size:24
Alignment explanation
Indices: 8961--9015 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
8951 ATGGCCTCGG
8961 TCGGATGGCCTCGGTCGGATGGCC
1 TCGGATGGCCTCGGTCGGATGGCC
*
8985 TCGGATGGCCTCGGTCGGATGGTC
1 TCGGATGGCCTCGGTCGGATGGCC
9009 TCGGATG
1 TCGGATG
9016 CCCAGCGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.09, C:0.25, G:0.42, T:0.24
Consensus pattern (24 bp):
TCGGATGGCCTCGGTCGGATGGCC
Found at i:9092 original size:29 final size:29
Alignment explanation
Indices: 9055--9112 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
9045 GCAATCTCTT
** *
9055 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCAGAAGACATGGCAACCTA
* *
9084 GTAGGTCGCCCAGAAGGCATGGCAACCTA
1 GTAGCTCGCCCAGAAGACATGGCAACCTA
9113 CGAAAAACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.28, G:0.33, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCAGAAGACATGGCAACCTA
Found at i:9331 original size:20 final size:19
Alignment explanation
Indices: 9291--9337 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
9281 TATTTTTTAA
*
9291 TTTTTTAAAATAGTATATAT
1 TTTTTTAAATTAGTAT-TAT
9311 TTATTTTAAATTA-TAATTAT
1 TT-TTTTAAATTAGT-ATTAT
9331 TTTTTTA
1 TTTTTTA
9338 TTTTGATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 8 0.33
21 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTTAAATTAGTATTAT
Found at i:14673 original size:2 final size:2
Alignment explanation
Indices: 14666--14691 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14656 AACATGTAGA
14666 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
14692 GCTTAACTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16103 original size:12 final size:12
Alignment explanation
Indices: 16086--16111 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16076 ATTGGAGGGC
16086 TGCTGCTGCTGT
1 TGCTGCTGCTGT
16098 TGCTGCTGCTGT
1 TGCTGCTGCTGT
16110 TG
1 TG
16112 TTGTTCACGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.35, T:0.42
Consensus pattern (12 bp):
TGCTGCTGCTGT
Found at i:17379 original size:21 final size:21
Alignment explanation
Indices: 17347--17415 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
17337 CCATCATGTT
*
17347 ATCAATCAACATAAACTACCAC
1 ATCAA-CAACATGAACTACCAC
* *
17369 ATCAACAACATGGACTACCAA
1 ATCAACAACATGAACTACCAC
* *
17390 ATCAACACCATGAATTACCAC
1 ATCAACAACATGAACTACCAC
17411 ATCAA
1 ATCAA
17416 GATCGTAACG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 35 0.88
22 5 0.12
ACGTcount: A:0.48, C:0.30, G:0.04, T:0.17
Consensus pattern (21 bp):
ATCAACAACATGAACTACCAC
Found at i:20054 original size:18 final size:18
Alignment explanation
Indices: 20027--20062 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20017 AGTCGAATAT
20027 TATTTCAACTATTTAAAA
1 TATTTCAACTATTTAAAA
* *
20045 TATTTGAACTTTTTAAAA
1 TATTTCAACTATTTAAAA
20063 ATAGTTTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (18 bp):
TATTTCAACTATTTAAAA
Found at i:20134 original size:45 final size:46
Alignment explanation
Indices: 20045--20214 Score: 135
Period size: 46 Copynumber: 3.5 Consensus size: 46
20035 CTATTTAAAA
* * * *
20045 TATTTGAACTTTTTAAAAATAGTTTAACTCGATCTGGGTTGAATAT
1 TATTTCAACTATTTAAAAATAGTTTAACTCGATCTGGATCGAATAT
*
20091 TATTTCAACTATTT-AAAATATTTTAACTCGATCTGGATCGAATAATTAAATAGT
1 TATTTCAACTATTTAAAAATAGTTTAACTCGATCTGGATCG--------AATA-T
* * * *
20145 TGATTTTTTAACAATTTAAAAATAGTTTAACTCGATATGGGTCGAATAT
1 T-A--TTTCAACTATTTAAAAATAGTTTAACTCGATCTGGATCGAATAT
*
20194 TATTTCAACTATTTTAAAATA
1 TATTTCAACTATTTAAAAATA
20215 TTAATTTATT
Statistics
Matches: 98, Mismatches: 13, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
45 23 0.23
46 28 0.29
48 1 0.01
49 2 0.02
50 4 0.04
53 4 0.04
54 2 0.02
55 1 0.01
57 10 0.10
58 23 0.23
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.42
Consensus pattern (46 bp):
TATTTCAACTATTTAAAAATAGTTTAACTCGATCTGGATCGAATAT
Found at i:27691 original size:30 final size:31
Alignment explanation
Indices: 27657--27730 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
27647 GTTTATTTAC
* *
27657 CAAAACA-GATTAAAACTGATAATTTAAATA
1 CAAAACATAATTAAAACTAATAATTTAAATA
*
27687 CAAAA-ATAATTCAAACTAATAATTTAAATA
1 CAAAACATAATTAAAACTAATAATTTAAATA
27717 CTAAACACATAATT
1 C-AAA-ACATAATT
27731 TTTACTAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.03
30 26 0.70
31 3 0.08
32 1 0.03
33 6 0.16
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (31 bp):
CAAAACATAATTAAAACTAATAATTTAAATA
Found at i:30985 original size:31 final size:32
Alignment explanation
Indices: 30950--31010 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
30940 ATAGTTTTGA
30950 AAAATTGAA-AGTTTAGGTACTAAA-ACATATC
1 AAAATT-AATAGTTTAGGTACTAAATACATATC
* *
30981 AAAATTAATATTTTAGGTATTAAATACATA
1 AAAATTAATAGTTTAGGTACTAAATACATA
31011 ATTTACCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.08
31 19 0.73
32 5 0.19
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (32 bp):
AAAATTAATAGTTTAGGTACTAAATACATATC
Found at i:32379 original size:30 final size:30
Alignment explanation
Indices: 32323--32383 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
32313 TTTTTACCCC
* *
32323 CTTGAATTTTATAAGTTCAAGTTCGCCTCT
1 CTTGAATTTTAAAAATTCAAGTTCGCCTCT
*
32353 CTTGAAATTTTAAAAATTTAAG-TCGCCTCT
1 CTTG-AATTTTAAAAATTCAAGTTCGCCTCT
32383 C
1 C
32384 CTAACATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (30 bp):
CTTGAATTTTAAAAATTCAAGTTCGCCTCT
Found at i:38270 original size:15 final size:15
Alignment explanation
Indices: 38250--38279 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38240 AAAAAATATT
*
38250 TTAAGGGTTAAAATA
1 TTAAGGGTCAAAATA
38265 TTAAGGGTCAAAATA
1 TTAAGGGTCAAAATA
38280 GATATAGTAA
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:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (15 bp):
TTAAGGGTCAAAATA
Found at i:40965 original size:38 final size:36
Alignment explanation
Indices: 40894--40965 Score: 85
Period size: 38 Copynumber: 1.9 Consensus size: 36
40884 GTATACATTT
*
40894 AATATTAAATTAATATTTTAATATCATTTTAATAAA
1 AATATTAAATTAATATTTTAATATCATTATAATAAA
40930 AATATTAATTATTAAT-TATTTAATATACA-TATAATA
1 AATATTAA--ATTAATAT-TTTAATAT-CATTATAATA
40966 TAATTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
36 8 0.26
37 1 0.03
38 20 0.65
39 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (36 bp):
AATATTAAATTAATATTTTAATATCATTATAATAAA
Found at i:40981 original size:46 final size:47
Alignment explanation
Indices: 40912--41008 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 47
40902 ATTAATATTT
*
40912 TAATATCATTTTAATAAAAATATTA-ATTATTAATTATT-TAATATACATA
1 TAATATAATTTTAAT--AAATATTATATTATTAA-TATTATAATA-ACATA
* *
40961 TAATATAATTTTAAT-AATATTATATTTTTAATATTATATTAACATA
1 TAATATAATTTTAATAAATATTATATTATTAATATTATAATAACATA
41007 TA
1 TA
41009 CTCATATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
46 18 0.42
47 11 0.26
49 14 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (47 bp):
TAATATAATTTTAATAAATATTATATTATTAATATTATAATAACATA
Found at i:41000 original size:19 final size:18
Alignment explanation
Indices: 40958--41001 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
40948 TTTAATATAC
*
40958 ATATAATATAATTTTAAT
1 ATATATTATAATTTTAAT
*
40976 A-ATATTATATTTTTAAT
1 ATATATTATAATTTTAAT
40993 ATTATATTA
1 A-TATATTA
41002 ACATATACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATTATAATTTTAAT
Found at i:41195 original size:30 final size:27
Alignment explanation
Indices: 41141--41195 Score: 65
Period size: 30 Copynumber: 1.9 Consensus size: 27
41131 TGAGTAATAT
**
41141 TAATTTATATATTTAATATTAATACAA
1 TAATTTATATATTTAATAAAAATACAA
41168 TAATTTAGTATTATGTTAATAAAAATAC
1 TAATTTA-TA-TAT-TTAATAAAAATAC
41196 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 2 0.09
29 3 0.13
30 11 0.48
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (27 bp):
TAATTTATATATTTAATAAAAATACAA
Found at i:52434 original size:30 final size:30
Alignment explanation
Indices: 52394--52454 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
52384 ATGAGTGAAT
*
52394 TTGACCCAACAAGA-TTAATTTTTATATAAA
1 TTGACCCAACAA-ACTTAATTTCTATATAAA
* *
52424 TTGACTCAACAAACTTAATTTCTGTATAAA
1 TTGACCCAACAAACTTAATTTCTATATAAA
52454 T
1 T
52455 AGTTACAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.38
Consensus pattern (30 bp):
TTGACCCAACAAACTTAATTTCTATATAAA
Found at i:52594 original size:30 final size:31
Alignment explanation
Indices: 52560--52633 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
52550 TTAAAAAACA
*
52560 TAAGATATGATCACTTT-GTTTTTATTTAAT
1 TAAGATATGATCACTTTCATTTTTATTTAAT
*
52590 TAAGATATGGTCACTTTCATTTTTATTTAAT
1 TAAGATATGATCACTTTCATTTTTATTTAAT
*
52621 TAAGATGTGATCA
1 TAAGATATGATCA
52634 TCATTAGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 16 0.41
31 23 0.59
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (31 bp):
TAAGATATGATCACTTTCATTTTTATTTAAT
Found at i:53309 original size:23 final size:24
Alignment explanation
Indices: 53274--53323 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
53264 ATAAGTTAAG
*
53274 ATAAAATTTTAAAGTTAA-TATAT
1 ATAAAATTATAAAGTTAAGTATAT
* * *
53297 ATAATATTATAAATTTAAGTATTT
1 ATAAAATTATAAAGTTAAGTATAT
53321 ATA
1 ATA
53324 CACTAAGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATAAAATTATAAAGTTAAGTATAT
Done.