Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009363.1 Hibiscus syriacus cultivar Beakdansim tig00113187_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: 67187
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3927 original size:18 final size:18
Alignment explanation
Indices: 3901--3944 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3891 GTGAAGTATG
* *
3901 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGGCGTGGCA
*
3919 AATGTTGTTGGCGTGGTA
1 AATGTTGTTGGCGTGGCA
*
3937 AGTGTTGT
1 AATGTTGT
3945 AATATTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.07, G:0.39, T:0.39
Consensus pattern (18 bp):
AATGTTGTTGGCGTGGCA
Found at i:8555 original size:14 final size:14
Alignment explanation
Indices: 8536--8565 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8526 GGTGATGAAC
8536 TATGGTAATGGAAA
1 TATGGTAATGGAAA
*
8550 TATGGTGATGGAAA
1 TATGGTAATGGAAA
8564 TA
1 TA
8566 GTATCTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (14 bp):
TATGGTAATGGAAA
Found at i:17141 original size:19 final size:21
Alignment explanation
Indices: 17098--17149 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
17088 GAAACCCCTT
17098 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
17119 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
17138 TGAAGATACATG
1 TGAAAATACATG
17150 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:25798 original size:15 final size:16
Alignment explanation
Indices: 25761--25817 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
25751 CAAATAAGAT
25761 AATGAAAT-AAGA-AA
1 AATGAAATAAAGAGAA
* *
25775 AGATAAAATAAA-AGGA
1 A-ATGAAATAAAGAGAA
25791 AATGAAATAAAGAGAA
1 AATGAAATAAAGAGAA
25807 AATGAAGATAA
1 AATGAA-ATAA
25818 CTTACAACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 1 0.03
15 16 0.47
16 13 0.38
17 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (16 bp):
AATGAAATAAAGAGAA
Found at i:25956 original size:24 final size:25
Alignment explanation
Indices: 25906--25972 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
25896 TTGTTTTGTG
*
25906 CTTCTCTTTGACTTTGCAACTTTTT
1 CTTCTCTTTGACTTTGCAAATTTTT
*
25931 CTTCTTTTTG-CTTTG-AAATTTCTT
1 CTTCTCTTTGACTTTGCAAATTT-TT
* * *
25955 CTTTTCTTTTATTTTGCA
1 CTTCTCTTTGACTTTGCA
25973 CTCCAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 5 0.15
24 14 0.42
25 13 0.39
26 1 0.03
ACGTcount: A:0.12, C:0.19, G:0.07, T:0.61
Consensus pattern (25 bp):
CTTCTCTTTGACTTTGCAAATTTTT
Found at i:31680 original size:22 final size:24
Alignment explanation
Indices: 31635--31680 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
31625 CTCTTCCAAA
31635 TGATCCCTAATAAAATAATAAATC
1 TGATCCCTAATAAAATAATAAATC
* *
31659 TGAT-CCTAA-AAGATAATTAATC
1 TGATCCCTAATAAAATAATAAATC
31681 ATCCTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 5 0.25
24 4 0.20
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (24 bp):
TGATCCCTAATAAAATAATAAATC
Found at i:33054 original size:11 final size:13
Alignment explanation
Indices: 33022--33051 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
33012 TGGCCAAAGA
33022 TGAAAAGGTATGT
1 TGAAAAGGTATGT
33035 TGAAAAGGTATG-
1 TGAAAAGGTATGT
33047 TGAAA
1 TGAAA
33052 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:38750 original size:15 final size:15
Alignment explanation
Indices: 38714--38743 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38704 GTGCTTCAAC
38714 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
38728 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
38743 T
1 T
38744 CTTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:38766 original size:27 final size:28
Alignment explanation
Indices: 38736--38797 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
38726 CTTTTCTTTG
* *
38736 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
*
38763 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGCTTCAATTT
38791 CTTTTCT
1 CTTTTCT
38798 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 8 0.28
29 4 0.14
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAATTT
Found at i:45600 original size:11 final size:11
Alignment explanation
Indices: 45586--45641 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
45576 CTATTTTGAA
45586 TTTCTTTTTCT
1 TTTCTTTTTCT
45597 TTTCTTTTTTTCT
1 TTTC--TTTTTCT
*
45610 GATTCTTCTTT-T
1 -TTTCTT-TTTCT
*
45622 TGTCTTTTTCT
1 TTTCTTTTTCT
45633 TTTCTTTTT
1 TTTCTTTTT
45642 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
10 3 0.08
11 17 0.47
12 3 0.08
13 10 0.28
14 3 0.08
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:49833 original size:24 final size:24
Alignment explanation
Indices: 49806--49859 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
49796 ATCAGCAAAT
* *
49806 AAAAGTCAAGCATTCCAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAGAAG
* *
49830 AAAAATCCAGCACTCAAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAGAAG
49854 AAAAGT
1 AAAAGT
49860 AAAGAAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.17, G:0.15, T:0.11
Consensus pattern (24 bp):
AAAAGTCAAGCACTCAAAAAGAAG
Found at i:51162 original size:24 final size:25
Alignment explanation
Indices: 51116--51170 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
51106 ACAATTATGC
*
51116 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
51140 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
51165 CA-TTGA
1 CACTTGA
51171 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:57034 original size:14 final size:14
Alignment explanation
Indices: 57017--57067 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
57007 TATTTTTGGA
57017 TTTCTTCTTTTTCT
1 TTTCTTCTTTTTCT
57031 TTTCTTCTTTTT-T
1 TTTCTTCTTTTTCT
*
57044 TTT-TTGTCTTTTC-
1 TTTCTTCT-TTTTCT
57057 TTTCTT-TTTTT
1 TTTCTTCTTTTT
57068 GTACTCCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 7 0.21
13 12 0.36
14 14 0.42
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTCTTCTTTTTCT
Found at i:57054 original size:22 final size:22
Alignment explanation
Indices: 57024--57067 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
57014 GGATTTCTTC
57024 TTTTTCTTTTC-TTCTTTTTTT
1 TTTTTCTTTTCTTTCTTTTTTT
57045 TTTTGTCTTTTCTTTCTTTTTTT
1 TTTT-TCTTTTCTTTCTTTTTTT
57068 GTACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
22 7 0.33
23 10 0.48
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTTCTTTTCTTTCTTTTTTT
Found at i:64950 original size:24 final size:24
Alignment explanation
Indices: 64918--64966 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
64908 TCATCCTAAC
*
64918 ACCCTTGACGCCTAGACAAGTCCA
1 ACCCTTGACACCTAGACAAGTCCA
64942 ACCCTTGACACCTAGACAAGTCCA
1 ACCCTTGACACCTAGACAAGTCCA
64966 A
1 A
64967 ATTGATCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.37, G:0.14, T:0.16
Consensus pattern (24 bp):
ACCCTTGACACCTAGACAAGTCCA
Done.