Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008401.1 Hibiscus syriacus cultivar Beakdansim tig00111170_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: 94450
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6818 original size:9 final size:9
Alignment explanation
Indices: 6804--6906 Score: 80
Period size: 9 Copynumber: 10.8 Consensus size: 9
6794 GGCTGCTGGA
6804 AACCGGTTT
1 AACCGGTTT
6813 AACCGGTTTT
1 AACCGG-TTT
6823 CAACCGGTTCT
1 -AACCGGTT-T
*
6834 GACCGGTTT
1 AACCGGTTT
* *
6843 GACCGGTTCG
1 AACCGGTT-T
6853 AACCGGTTT
1 AACCGGTTT
* *
6862 GACCGGTTCG
1 AACCGGTT-T
6872 AACCGGTTT
1 AACCGGTTT
* *
6881 GACCGGTCTG
1 AACCGGT-TT
6891 AACCGGTTT
1 AACCGGTTT
*
6900 GACCGGT
1 AACCGGT
6907 CAGACCCGAC
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
9 35 0.47
10 33 0.44
11 7 0.09
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:6829 original size:11 final size:10
Alignment explanation
Indices: 6804--6899 Score: 56
Period size: 10 Copynumber: 9.9 Consensus size: 10
6794 GGCTGCTGGA
6804 AACCGG-TTT
1 AACCGGTTTT
6813 AACCGGTTTT
1 AACCGGTTTT
*
6823 CAACCGGTTCT
1 -AACCGGTTTT
*
6834 GACCGG-TTT
1 AACCGGTTTT
* **
6843 GACCGGTTCG
1 AACCGGTTTT
6853 AACCGG-TTT
1 AACCGGTTTT
* **
6862 GACCGGTTCG
1 AACCGGTTTT
6872 AACCGG-TTT
1 AACCGGTTTT
* * *
6881 GACCGGTCTG
1 AACCGGTTTT
6891 AACCGGTTT
1 AACCGGTTT
6900 GACCGGTCAG
Statistics
Matches: 63, Mismatches: 19, Indels: 9
0.69 0.21 0.10
Matches are distributed among these distances:
9 26 0.41
10 28 0.44
11 9 0.14
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (10 bp):
AACCGGTTTT
Found at i:6829 original size:20 final size:21
Alignment explanation
Indices: 6804--6880 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 21
6794 GGCTGCTGGA
6804 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
6824 AACCGGTTCTGACCGG-TTT-
1 AACCGGTTCTAACCGGTTTTC
* *
6843 GACCGGTTCGAACCGG-TTT-
1 AACCGGTTCTAACCGGTTTTC
* *
6862 GACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
6881 GACCGGTCTG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 32 0.63
20 13 0.25
21 6 0.12
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:6849 original size:19 final size:19
Alignment explanation
Indices: 6825--6906 Score: 132
Period size: 19 Copynumber: 4.3 Consensus size: 19
6815 CCGGTTTTCA
6825 ACCGGTTCTG-ACCGGTTTG
1 ACCGGTTC-GAACCGGTTTG
6844 ACCGGTTCGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTG
6863 ACCGGTTCGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTG
6882 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTC-GAACCGGTTTG
6901 ACCGGT
1 ACCGGT
6907 CAGACCCGAC
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
18 3 0.05
19 57 0.95
ACGTcount: A:0.15, C:0.27, G:0.32, T:0.27
Consensus pattern (19 bp):
ACCGGTTCGAACCGGTTTG
Found at i:6919 original size:5 final size:5
Alignment explanation
Indices: 6909--6966 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
6899 TGACCGGTCA
* *
6909 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
6958 GACCC GACC
1 GACCC GACC
6967 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:6935 original size:22 final size:22
Alignment explanation
Indices: 6909--6973 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
6899 TGACCGGTCA
6909 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
6931 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
6953 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
6974 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:11376 original size:37 final size:37
Alignment explanation
Indices: 11303--11377 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
11293 GTTAGAAAAT
* *
11303 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
11340 ATTTATATAAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT--ATTTTCTTTAAAAAATTGAAAATCATAAA
11377 A
1 A
11378 AGGTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 14 0.42
39 5 0.15
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:17042 original size:14 final size:17
Alignment explanation
Indices: 17019--17059 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
17009 AACATAACCT
17019 ATAC-AAAGAAA-CA-A
1 ATACAAAAGAAACCATA
17033 AT-CAAAAGAAACCATA
1 ATACAAAAGAAACCATA
17049 ATACAAAAGAA
1 ATACAAAAGAA
17060 TTAAATACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 9 0.39
15 2 0.09
16 3 0.13
17 8 0.35
ACGTcount: A:0.68, C:0.15, G:0.07, T:0.10
Consensus pattern (17 bp):
ATACAAAAGAAACCATA
Found at i:25336 original size:4 final size:4
Alignment explanation
Indices: 25327--26764 Score: 2402
Period size: 4 Copynumber: 361.0 Consensus size: 4
25317 TATTTTGCTT
25327 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25375 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25423 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25471 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25519 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25567 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25615 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25663 CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25709 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25757 CATA CATA CATA CATA CATA CATA CATA CAT- -ATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25803 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
25851 CATA CATA CATA CATA CATA CATG CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * *
25899 CATA CATG CATG CATG CATG CATG CATG CATG CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
25947 CATA CATA CATA CATG CATG CATG CATG CATG CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
25995 CATG CATG CATG CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
26043 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
26091 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
26139 CATA CATA CATA CATA CATA CATG CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
26187 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
26235 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
26283 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT- -ATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
26329 CATA CATG CATA CATG CATA CATA CATG CATG CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
26377 CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
26425 CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
26473 CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
26521 CATA CATA CATG CATA CATA CATG CATA CATA CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
26569 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
26617 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
26665 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
26713 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
26761 CATA
1 CATA
26765 TAAACTAACT
Statistics
Matches: 1362, Mismatches: 66, Indels: 12
0.95 0.05 0.01
Matches are distributed among these distances:
2 6 0.00
4 1356 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:40768 original size:2 final size:2
Alignment explanation
Indices: 40761--40792 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40751 ATTATAACAT
40761 TA TA TA 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
40793 GGGGTTCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43738 original size:2 final size:2
Alignment explanation
Indices: 43731--43762 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43721 AATATGTTTT
43731 TA TA TA 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
43763 AATACTTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60043 original size:30 final size:31
Alignment explanation
Indices: 59995--60057 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
59985 AAAGTACCAT
*
59995 AAATATATAATTATTAATAATAAAAAAAGAAA
1 AAATATATAACTATTAATAA-AAAAAAAGAAA
**
60027 AAATATA-AACTA-TAATAAATTAAAAGAAA
1 AAATATATAACTATTAATAAAAAAAAAGAAA
60056 AA
1 AA
60058 TAATGAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.39
30 6 0.21
31 4 0.14
32 7 0.25
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (31 bp):
AAATATATAACTATTAATAAAAAAAAAGAAA
Found at i:61503 original size:22 final size:22
Alignment explanation
Indices: 61476--61518 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
61466 ATTATCACGT
*
61476 GTTTAAAACTTT-AAATCCTAA
1 GTTTTAAACTTTAAAATCCTAA
*
61497 GTTTTAAGCTTTAAAATCCTAA
1 GTTTTAAACTTTAAAATCCTAA
61519 TCTATAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (22 bp):
GTTTTAAACTTTAAAATCCTAA
Found at i:68493 original size:21 final size:21
Alignment explanation
Indices: 68464--68503 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
68454 GGTAGATCTC
* *
68464 TGATCGATGATTGGTAGAATA
1 TGATAGATGACTGGTAGAATA
68485 TGATAGATGACTGGTAGAA
1 TGATAGATGACTGGTAGAA
68504 GACGATGGAG
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:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (21 bp):
TGATAGATGACTGGTAGAATA
Found at i:72611 original size:13 final size:13
Alignment explanation
Indices: 72593--72617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72583 CTTTGGCCAT
72593 GATCAACACGACG
1 GATCAACACGACG
72606 GATCAACACGAC
1 GATCAACACGAC
72618 TTTCAACCTA
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:0.40, C:0.32, G:0.20, T:0.08
Consensus pattern (13 bp):
GATCAACACGACG
Found at i:86979 original size:27 final size:28
Alignment explanation
Indices: 86934--86991 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 28
86924 GCTTAATCAA
*
86934 TGAGTGTGTTTTAGTGTTTTAAACATTG
1 TGAGTGTGTTTTAGTGTTTTAAACATCG
86962 TGAGTGT-TTTTAGTGTTTTAAACATCG
1 TGAGTGTGTTTTAGTGTTTTAAACATCG
86989 TGA
1 TGA
86992 TTAGTTAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.48
Consensus pattern (28 bp):
TGAGTGTGTTTTAGTGTTTTAAACATCG
Found at i:88461 original size:4 final size:4
Alignment explanation
Indices: 88454--88549 Score: 174
Period size: 4 Copynumber: 24.0 Consensus size: 4
88444 TATATATATA
* *
88454 TATG TATG TATG AATA TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
88502 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
88550 GTGTACTTTT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 88 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:89368 original size:2 final size:2
Alignment explanation
Indices: 89361--89410 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
89351 TATCGGGCCG
* * * *
89361 AT AT AT AT AT AT TT AA AT -T AA AT AT AT AA AT AT -T 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
89401 AT AT AT AT AT
1 AT AT AT AT AT
89411 TTAATTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89387 original size:17 final size:17
Alignment explanation
Indices: 89365--89421 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
89355 GGGCCGATAT
89365 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
* *
89382 ATATATAAATATTATATATAT
1 ATATAT--AT-TTAAAT-TAA
*
89403 ATATATATTTAATTTAA
1 ATATATATTTAAATTAA
89420 AT
1 AT
89422 TAAATTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 10 0.32
18 4 0.13
19 4 0.13
20 5 0.16
21 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:92294 original size:12 final size:13
Alignment explanation
Indices: 92260--92301 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
92250 GTGGTATCCC
92260 TTGAT-ATTGATA
1 TTGATGATTGATA
92272 TTGAT-ATTGATA
1 TTGATGATTGATA
*
92284 TTGATGA-TGATG
1 TTGATGATTGATA
92296 TTGATG
1 TTGATG
92302 TTACTGTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 27 0.96
13 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (13 bp):
TTGATGATTGATA
Found at i:92303 original size:6 final size:6
Alignment explanation
Indices: 92260--92288 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
92250 GTGGTATCCC
92260 TTGATA TTGATA TTGATA TTGATA TTGAT
1 TTGATA TTGATA TTGATA TTGATA TTGAT
92289 GATGATGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
TTGATA
Done.