Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004174.1 Hibiscus syriacus cultivar Beakdansim tig00009129_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: 66285
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2048 original size:13 final size:13
Alignment explanation
Indices: 2026--2055 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2016 ACTAAACACC
2026 TTTC-ACATACCT
1 TTTCAACATACCT
2038 TTTCAACATACCT
1 TTTCAACATACCT
2051 TTTCA
1 TTTCA
2056 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:6104 original size:35 final size:35
Alignment explanation
Indices: 6065--6215 Score: 151
Period size: 35 Copynumber: 4.2 Consensus size: 35
6055 ATTACTGGTT
* *
6065 ATATAGGCGTTAAATGGTGATAGAAGTTGGTGATG
1 ATATAGGCGTAAAATGGTGATGGAAGTTGGTGATG
**
6100 ATATAGGCGTGCAATGGTGATGGAA-TATGGTGATG
1 ATATAGGCGTAAAATGGTGATGGAAGT-TGGTGATG
* *
6135 TTATAGGCGTGAAAATGGTGATGGAAGATGGTGATG
1 ATATAGGCGT-AAAATGGTGATGGAAGTTGGTGATG
* * * *
6171 TTATAGGAATGAAAAAATGGTGATGGAAGATGGTGATG
1 ATATAGG--CG-TAAAATGGTGATGGAAGTTGGTGATG
*
6209 TTATAGG
1 ATATAGG
6216 TAGTATCTTA
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
34 1 0.01
35 39 0.39
36 28 0.28
38 33 0.33
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.29
Consensus pattern (35 bp):
ATATAGGCGTAAAATGGTGATGGAAGTTGGTGATG
Found at i:6131 original size:13 final size:13
Alignment explanation
Indices: 6113--6170 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
6103 TAGGCGTGCA
6113 ATGGTGATGGAAT
1 ATGGTGATGGAAT
**
6126 ATGGTGATGTTAT
1 ATGGTGATGGAAT
* *
6139 A-GGCG-T-GAAA
1 ATGGTGATGGAAT
*
6149 ATGGTGATGGAAG
1 ATGGTGATGGAAT
6162 ATGGTGATG
1 ATGGTGATG
6171 TTATAGGAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 24 0.71
ACGTcount: A:0.29, C:0.02, G:0.40, T:0.29
Consensus pattern (13 bp):
ATGGTGATGGAAT
Found at i:6197 original size:38 final size:36
Alignment explanation
Indices: 6076--6215 Score: 174
Period size: 38 Copynumber: 3.9 Consensus size: 36
6066 TATAGGCGTT
* * * **
6076 AAATGGTGATAGAAGTTGGTGATGATATAGGCGTG-
1 AAATGGTGATGGAAGATGGTGATGTTATAGGAATGA
* * **
6111 CAATGGTGATGGAATATGGTGATGTTATAGGCGTGA
1 AAATGGTGATGGAAGATGGTGATGTTATAGGAATGA
6147 AAATGGTGATGGAAGATGGTGATGTTATAGGAATGAAA
1 AAATGGTGATGGAAGATGGTGATGTTATAGGAATG--A
6185 AAATGGTGATGGAAGATGGTGATGTTATAGG
1 AAATGGTGATGGAAGATGGTGATGTTATAGG
6216 TAGTATCTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
35 30 0.32
36 31 0.33
38 32 0.34
ACGTcount: A:0.33, C:0.02, G:0.36, T:0.29
Consensus pattern (36 bp):
AAATGGTGATGGAAGATGGTGATGTTATAGGAATGA
Found at i:6210 original size:74 final size:70
Alignment explanation
Indices: 6066--6215 Score: 192
Period size: 71 Copynumber: 2.1 Consensus size: 70
6056 TTACTGGTTA
* * ** * *
6066 TATAGGCGTTAAATGGTGATAGAAGTTGGTGATGATATAGGCGTGCAATGGTGATGGAATATGGT
1 TATAGGCGTAAAATGGTGATAGAAGATGGTGATGATATAGGAATGAAATGGTGATGGAAGATGGT
6131 GATGT
66 GATGT
* *
6136 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGTTATAGGAATGAAAAAATGGTGATGGAAGA
1 TATAGGCGT-AAAATGGTGATAGAAGATGGTGATGATATAGGAATG---AAATGGTGATGGAAGA
6201 TGGTGATGT
62 TGGTGATGT
6210 TATAGG
1 TATAGG
6216 TAGTATCTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
70 9 0.13
71 30 0.44
74 29 0.43
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.29
Consensus pattern (70 bp):
TATAGGCGTAAAATGGTGATAGAAGATGGTGATGATATAGGAATGAAATGGTGATGGAAGATGGT
GATGT
Found at i:10469 original size:26 final size:26
Alignment explanation
Indices: 10424--10475 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
10414 AAGTTGTTAA
10424 ATAAATGGATAATTAAGAAA-GGAAAT
1 ATAAATGGATAATT-AGAAATGGAAAT
10450 ATAAATGGAAATAATT-GAAATGGAAA
1 ATAAATGG--ATAATTAGAAATGGAAA
10476 GAAATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 12 0.52
27 5 0.22
28 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (26 bp):
ATAAATGGATAATTAGAAATGGAAAT
Found at i:10726 original size:36 final size:35
Alignment explanation
Indices: 10628--10746 Score: 148
Period size: 35 Copynumber: 3.4 Consensus size: 35
10618 TTGTTGGTTA
* * * * *
10628 TATAGGCATAAAATGGTGATAGAAGTTGGTGATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
10663 TATAGGCGTGCAATGATGATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
*
10698 TATAGACGTGAATATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGAA-ATGGTGATGGAAGATGGTGATGT
*
10734 TGTAGGCGTGAAA
1 TATAGGCGTGAAA
10747 AAATGGTGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 39 0.55
36 32 0.45
ACGTcount: A:0.32, C:0.04, G:0.35, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:13893 original size:11 final size:13
Alignment explanation
Indices: 13861--13890 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13851 TGGCCAAAGA
13861 TGAAAAGGTATGT
1 TGAAAAGGTATGT
13874 TGAAAAGGTATG-
1 TGAAAAGGTATGT
13886 TGAAA
1 TGAAA
13891 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:18132 original size:20 final size:19
Alignment explanation
Indices: 18097--18138 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
18087 AGCATTTATC
*
18097 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTATT
*
18116 TTCATTAAAAATCATGTGTT
1 TTCATT-AAAATCATGTATT
18136 TTC
1 TTC
18139 GAAGGAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:30030 original size:35 final size:35
Alignment explanation
Indices: 29991--30066 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
29981 ATGATAATGG
* *
29991 GATGGTGATTATATAGGCGTGAAATGGAGATGGAA
1 GATGGTGATGATATAGGCATGAAATGGAGATGGAA
* * *
30026 GATGGTGATGATATAGGCATGATATGGATATGGGA
1 GATGGTGATGATATAGGCATGAAATGGAGATGGAA
30061 GATGGT
1 GATGGT
30067 ATGGATAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.03, G:0.38, T:0.28
Consensus pattern (35 bp):
GATGGTGATGATATAGGCATGAAATGGAGATGGAA
Found at i:32736 original size:17 final size:17
Alignment explanation
Indices: 32716--32774 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
32706 TTTAGGGAAG
32716 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
32733 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
32749 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
32766 TAGTTCATT
1 TAGTTCATT
32775 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:34852 original size:35 final size:34
Alignment explanation
Indices: 34813--34928 Score: 160
Period size: 35 Copynumber: 3.3 Consensus size: 34
34803 TGGTAAGGGA
* *
34813 ATGGTGATGATATAGGCGTGATATGGTGATAGTAG
1 ATGGTGATGATATAGGCGTGAAATGGTGAT-GAAG
*
34848 ATGGTGATGATATAGGCGTGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGAT-GAAG
*
34883 ATGGTGATGTTATAGGCGTGAAAATGGTGATGAAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATG-AAG
34919 ATGGTGATGA
1 ATGGTGATGA
34929 ACAAATAGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
35 51 0.71
36 21 0.29
ACGTcount: A:0.30, C:0.03, G:0.38, T:0.28
Consensus pattern (34 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGAAG
Found at i:34924 original size:13 final size:13
Alignment explanation
Indices: 34870--34929 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
34860 TAGGCGTGCA
*
34870 ATGGTGATGGAAG
1 ATGGTGATGAAAG
** *
34883 ATGGTGATGTTAT
1 ATGGTGATGAAAG
*
34896 A-GGCG-TGAAA-
1 ATGGTGATGAAAG
34906 ATGGTGATGAAAG
1 ATGGTGATGAAAG
34919 ATGGTGATGAA
1 ATGGTGATGAA
34930 CAAATAGTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 1 0.03
11 6 0.16
12 8 0.22
13 22 0.59
ACGTcount: A:0.33, C:0.02, G:0.38, T:0.27
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:35311 original size:19 final size:20
Alignment explanation
Indices: 35270--35320 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
35260 GAAACCCCTT
* *
35270 TGAAAATACATGATTTTTTA
1 TGAAAATACATGAATTTTAA
35290 TGAAAATACAT-AATTTTAA
1 TGAAAATACATGAATTTTAA
*
35309 TGAAGATACATG
1 TGAAAATACATG
35321 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGAATTTTAA
Found at i:38956 original size:35 final size:35
Alignment explanation
Indices: 38911--39026 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
38901 TGGTAAGGGA
*
38911 ATGGTGATGATATAGGTGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGTGTGAAATGGTGATGGAAG
*
38946 ATGGTGATGATATAGGTGTGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGTGTGAAATGGTGATGGAAG
* *
38981 ATGGTGATGTTATAGGAGTGAAAATGGTGATGGAAG
1 ATGGTGATGATATAGGTGTG-AAATGGTGATGGAAG
39017 ATGGTGATGA
1 ATGGTGATGA
39027 ACATATAGTA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 51 0.69
36 23 0.31
ACGTcount: A:0.32, C:0.01, G:0.39, T:0.28
Consensus pattern (35 bp):
ATGGTGATGATATAGGTGTGAAATGGTGATGGAAG
Found at i:38986 original size:13 final size:13
Alignment explanation
Indices: 38968--39025 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
38958 TAGGTGTGCA
38968 ATGGTGATGGAAG
1 ATGGTGATGGAAG
** *
38981 ATGGTGATGTTAT
1 ATGGTGATGGAAG
* *
38994 A-GGAG-T-GAAA
1 ATGGTGATGGAAG
39004 ATGGTGATGGAAG
1 ATGGTGATGGAAG
39017 ATGGTGATG
1 ATGGTGATG
39026 AACATATAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 23 0.70
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:39416 original size:19 final size:20
Alignment explanation
Indices: 39369--39419 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
39359 GAAACCCCTT
**
39369 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
39389 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
39408 TGAAGATACATG
1 TGAAAATACATG
39420 CTCTTTGTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:41349 original size:2 final size:2
Alignment explanation
Indices: 41342--41379 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
41332 AGTTATTTTC
*
41342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41380 GTTATTATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46287 original size:22 final size:22
Alignment explanation
Indices: 46259--46300 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
46249 AGTGAAACTG
*
46259 AAATTAATCAGAACCAAAATCA
1 AAATTAACCAGAACCAAAATCA
*
46281 AAATTAACCCGAACCAAAAT
1 AAATTAACCAGAACCAAAAT
46301 TTAACCCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.21, G:0.05, T:0.17
Consensus pattern (22 bp):
AAATTAACCAGAACCAAAATCA
Found at i:50942 original size:13 final size:13
Alignment explanation
Indices: 50924--50983 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
50914 TCTTCTTGAA
50924 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
*
50937 TTCTTTTCTTCTT
1 TTCTTTTTTTCTT
* *
50950 TTCTGATTTTTCTC
1 TTCT-TTTTTTCTT
*
50964 TTCTTTTTGTCTTT
1 TTCTTTTTTTC-TT
50978 TTCTTT
1 TTCTTT
50984 CGTTTTGCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 21 0.55
14 17 0.45
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:54065 original size:21 final size:24
Alignment explanation
Indices: 54023--54067 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
54013 AAATAAACAA
54023 AAGATAAATAAACGGAAGATGAAAT
1 AAGATAAATAAAC-GAAGATGAAAT
54048 AAGAT-AATAAA-GAA-ATGAAA
1 AAGATAAATAAACGAAGATGAAA
54068 AGATATCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
22 3 0.15
24 6 0.30
25 5 0.25
ACGTcount: A:0.64, C:0.02, G:0.18, T:0.16
Consensus pattern (24 bp):
AAGATAAATAAACGAAGATGAAAT
Found at i:63408 original size:22 final size:22
Alignment explanation
Indices: 63372--63415 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
63362 CAAGTGCTAC
* *
63372 AAAAAAGCAACAAGAAAAAAAA
1 AAAAAAACAAAAAGAAAAAAAA
*
63394 AAAAAAACAAAAAGAAAGAAAA
1 AAAAAAACAAAAAGAAAAAAAA
63416 TACTCCTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAGAAAAAAAA
Done.