Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004013.1 Hibiscus syriacus cultivar Beakdansim tig00008754_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: 46593
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:166 original size:30 final size:31
Alignment explanation
Indices: 130--189 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
120 TCTTGCTTGC
130 ACTAACTC-GTTTCTCT-ATTTTGTTTGTGTT
1 ACTAACTCAGTTTCTCTCA-TTTGTTTGTGTT
* *
160 ACTAACTCATTTTTTCTCATTTGTTTGTGT
1 ACTAACTCAGTTTCTCTCATTTGTTTGTGT
190 CATTTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.57
Consensus pattern (31 bp):
ACTAACTCAGTTTCTCTCATTTGTTTGTGTT
Found at i:4378 original size:105 final size:105
Alignment explanation
Indices: 4191--4379 Score: 290
Period size: 105 Copynumber: 1.8 Consensus size: 105
4181 TGAGAATTTT
* *
4191 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
4256 TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
66 TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
* * * *
4296 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCAC-
* *
4361 TT-AAACAAAGTTGATCTCA
65 TTAAAACAAAATTAATCTCA
4380 TCATTGTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
105 73 0.97
106 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (105 bp):
AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
Found at i:5996 original size:18 final size:19
Alignment explanation
Indices: 5920--6073 Score: 101
Period size: 18 Copynumber: 8.2 Consensus size: 19
5910 AATTGAAAAA
5920 ATATAATATATATATAAA--
1 ATATAATATAT-TATAAACT
*
5938 ATAAAAT-TATATATAAACT
1 ATATAATATAT-TATAAACT
*
5957 ATAT-TTATATTATAAACT
1 ATATAATATATTATAAACT
5975 ATATAAT-TATTATAAACT
1 ATATAATATATTATAAACT
**
5993 ATAT-ATCA-ATTAT-ATTT
1 ATATAAT-ATATTATAAACT
*
6010 ATGTGAACTATATATATAAACT
1 ATAT-AA-TATAT-TATAAACT
* *
6032 ATGTATATAAAATTATAAACT
1 ATATA-AT-ATATTATAAACT
*
6053 ATATAAT-TATTATAAGCT
1 ATATAATATATTATAAACT
6071 ATA
1 ATA
6074 GATATAAATT
Statistics
Matches: 109, Mismatches: 13, Indels: 28
0.73 0.09 0.19
Matches are distributed among these distances:
17 17 0.16
18 51 0.47
19 9 0.08
20 5 0.05
21 17 0.16
22 10 0.09
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (19 bp):
ATATAATATATTATAAACT
Found at i:6033 original size:13 final size:13
Alignment explanation
Indices: 6015--6130 Score: 76
Period size: 13 Copynumber: 8.8 Consensus size: 13
6005 TATTTATGTG
6015 AACTATATATATA
1 AACTATATATATA
*
6028 AACTATGTATATAA
1 AACTATATATAT-A
* *
6042 AATTATAAACTATA
1 AACTATATA-TATA
6056 TAA-T-TAT-TATA
1 -AACTATATATATA
* *
6067 AGCTATAGATATA
1 AACTATATATATA
* * * *
6080 AATTATGTTTATGTG
1 AACTA--TATATATA
6095 AACTATATATATA
1 AACTATATATATA
*
6108 AACTATGTATATA
1 AACTATATATATA
6121 AACTATATAT
1 AACTATATAT
6131 GTATAAAATA
Statistics
Matches: 76, Mismatches: 19, Indels: 16
0.68 0.17 0.14
Matches are distributed among these distances:
10 1 0.01
11 5 0.07
12 2 0.03
13 46 0.61
14 9 0.12
15 13 0.17
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (13 bp):
AACTATATATATA
Found at i:6066 original size:78 final size:79
Alignment explanation
Indices: 5945--6122 Score: 274
Period size: 80 Copynumber: 2.3 Consensus size: 79
5935 AAAATAAAAT
* * *
5945 TATATATAAACTA--TAT-TTATATTATAAACTATATAATTATTATAAACTAT-ATATCAATTAT
1 TATATATAAACTATGTATATAAAATTATAAACTATATAATTATTATAAACTATAATATAAATTAT
6006 ATTTATGTGAACTA
66 ATTTATGTGAACTA
*
6020 TATATATAAACTATGTATATAAAATTATAAACTATATAATTATTATAAGCTATAGATATAAATTA
1 TATATATAAACTATGTATATAAAATTATAAACTATATAATTATTATAAACTATA-ATATAAATTA
*
6085 TGTTTATGTGAACTA
65 TATTTATGTGAACTA
6100 TATATATAAACTATGTATATAAA
1 TATATATAAACTATGTATATAAA
6123 CTATATATGT
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
75 13 0.14
77 3 0.03
78 31 0.33
80 46 0.49
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (79 bp):
TATATATAAACTATGTATATAAAATTATAAACTATATAATTATTATAAACTATAATATAAATTAT
ATTTATGTGAACTA
Found at i:6120 original size:15 final size:15
Alignment explanation
Indices: 6098--6245 Score: 59
Period size: 15 Copynumber: 10.3 Consensus size: 15
6088 TTATGTGAAC
6098 TATATATATAAAC--
1 TATATATATAAACTA
*
6111 TATGTATATAAACTA
1 TATATATATAAACTA
*
6126 TATATGTATAAA--A
1 TATATATATAAACTA
6139 TATA-A-A-AAGTA-TA
1 TATATATATAA--ACTA
* * *
6152 TAAACTATAAAAAGTA
1 TATA-TATATAAACTA
* *
6168 TATAGTTTATAAAATA
1 TATA-TATATAAACTA
* *
6184 TTATTTATATTAA-TA
1 -TATATATATAAACTA
6199 TAGTATATAT--A-TA
1 TA-TATATATAAACTA
6212 TATATATATAAACTA
1 TATATATATAAACTA
**
6227 TATAGGTATAAACTA
1 TATATATATAAACTA
6242 TATA
1 TATA
6246 AAATACATAG
Statistics
Matches: 104, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
10 2 0.02
11 1 0.01
12 8 0.08
13 26 0.25
14 3 0.03
15 39 0.38
16 20 0.19
17 5 0.05
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.40
Consensus pattern (15 bp):
TATATATATAAACTA
Found at i:6181 original size:18 final size:18
Alignment explanation
Indices: 6114--6171 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
6104 TATAAACTAT
* *
6114 GTATATAAACTAT-ATAT
1 GTATATAAACTATAAAAA
6131 GTATA-AAA-TATAAAAA
1 GTATATAAACTATAAAAA
6147 GTATATAAACTATAAAAA
1 GTATATAAACTATAAAAA
6165 GTATATA
1 GTATATA
6172 GTTTATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
15 3 0.08
16 10 0.28
17 8 0.22
18 15 0.42
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (18 bp):
GTATATAAACTATAAAAA
Found at i:6216 original size:17 final size:17
Alignment explanation
Indices: 6098--6221 Score: 51
Period size: 17 Copynumber: 7.2 Consensus size: 17
6088 TTATGTGAAC
*
6098 TATATATATAAACTAT-G
1 TATATATATATA-TATAG
*
6115 TATATAAACTATATAT-G
1 TATATATA-TATATATAG
* * *
6132 TATA-AAATATAAAAAG
1 TATATATATATATATAG
* * *
6148 TATATAAACTATAAAAAG
1 TATATATA-TATATATAG
* * *
6166 TATATAGTTTATAAAATAT
1 TATATA-TATAT-ATATAG
*
6185 TATTTATAT-TAATATAG
1 TATATATATAT-ATATAG
6202 TATATATATATATATA-
1 TATATATATATATATAG
6218 TATA
1 TATA
6222 AACTATATAG
Statistics
Matches: 87, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
15 5 0.06
16 12 0.14
17 37 0.43
18 24 0.28
19 9 0.10
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATATATATATAG
Found at i:6236 original size:17 final size:16
Alignment explanation
Indices: 6196--6245 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
6186 ATTTATATTA
*
6196 ATATAGTATATATA-T
1 ATATAGTATATAAACT
6211 ATATA-TATATAAACT
1 ATATAGTATATAAACT
*
6226 ATATAG-GTATAAACT
1 ATATAGTATATAAACT
6241 ATATA
1 ATATA
6246 AAATACATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.23
15 24 0.77
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (16 bp):
ATATAGTATATAAACT
Found at i:6414 original size:2 final size:2
Alignment explanation
Indices: 6409--6456 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
6399 TTATATAGTT
** *
6409 TA TA TA TA TA TA TA TA TA GG TA TA TA TA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
6452 CTA TA
1 -TA TA
6457 CATGGTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 35 0.92
3 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6456 original size:20 final size:19
Alignment explanation
Indices: 6400--6474 Score: 75
Period size: 20 Copynumber: 4.1 Consensus size: 19
6390 TAATTTACTT
6400 TATATAGTTTATATATATA
1 TATATAGTTTATATATATA
**
6419 TATATA---TAGGTATATA
1 TATATAGTTTATATATATA
6435 TATATAGTTTATATATACTA
1 TATATAGTTTATATATA-TA
* * *
6455 TACATGGTTTATACATATA
1 TATATAGTTTATATATATA
6474 T
1 T
6475 TAGGGTTTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
16 14 0.31
19 15 0.33
20 16 0.36
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (19 bp):
TATATAGTTTATATATATA
Found at i:6473 original size:33 final size:35
Alignment explanation
Indices: 6401--6473 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
6391 AATTTACTTT
* *
6401 ATATAGTTTATATATATATATATATAGGTATATAT
1 ATATAGTTTATATATATATATACATAGGTATATAC
* *
6436 ATATAGTTTATATATA-CTATACAT-GGTTTATAC
1 ATATAGTTTATATATATATATACATAGGTATATAC
6469 ATATA
1 ATATA
6474 TTAGGGTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 12 0.35
34 6 0.18
35 16 0.47
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (35 bp):
ATATAGTTTATATATATATATACATAGGTATATAC
Found at i:6486 original size:7 final size:7
Alignment explanation
Indices: 6474--6574 Score: 112
Period size: 7 Copynumber: 14.4 Consensus size: 7
6464 TATACATATA
6474 TTAGGGT
1 TTAGGGT
6481 TTAGGGT
1 TTAGGGT
6488 TTAGGGT
1 TTAGGGT
*
6495 TTAGTGT
1 TTAGGGT
*
6502 TTAGGTT
1 TTAGGGT
**
6509 TTAGTAT
1 TTAGGGT
6516 TTAGGGT
1 TTAGGGT
6523 TTAGGGT
1 TTAGGGT
*
6530 TTAGTGT
1 TTAGGGT
*
6537 TTATGGT
1 TTAGGGT
**
6544 TTAATGT
1 TTAGGGT
*
6551 TTAGAGT
1 TTAGGGT
6558 TTAGGGT
1 TTAGGGT
*
6565 TTAAGGT
1 TTAGGGT
6572 TTA
1 TTA
6575 TATAAACTAT
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 78 1.00
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:6841 original size:19 final size:20
Alignment explanation
Indices: 6804--6841 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6794 AATTTTTCTA
6804 TTCCCTCTAAATGTCCCAAT
1 TTCCCTCTAAATGTCCCAAT
6824 TTCCCTCTAAAT-TCCCAA
1 TTCCCTCTAAATGTCCCAA
6842 ATAAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.26, C:0.37, G:0.03, T:0.34
Consensus pattern (20 bp):
TTCCCTCTAAATGTCCCAAT
Found at i:6918 original size:2 final size:2
Alignment explanation
Indices: 6911--7016 Score: 164
Period size: 2 Copynumber: 53.5 Consensus size: 2
6901 ACTTTGAATA
6911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AGT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
6952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6993 AGT AT AT AC AT AT AT AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT A
7017 ATTAAACATA
Statistics
Matches: 97, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
1 3 0.03
2 92 0.95
3 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7458 original size:2 final size:2
Alignment explanation
Indices: 7451--7507 Score: 89
Period size: 2 Copynumber: 28.5 Consensus size: 2
7441 TATGTTTTAT
*
7451 TA TA TA TA TT TA TA TA TA TA CT- 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 TA TA TA TA TA
7493 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
7508 TCAAAGTGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 49 0.96
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:7606 original size:27 final size:27
Alignment explanation
Indices: 7576--7630 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
7566 TATTTTATTT
*
7576 GGGAAATTAGGAAATTTTGAGAAAATA
1 GGGAAATTAGGAAATTTAGAGAAAATA
* *
7603 GGGAAATTGGGAAATTTAGAGAGAATA
1 GGGAAATTAGGAAATTTAGAGAAAATA
7630 G
1 G
7631 AAAATTTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (27 bp):
GGGAAATTAGGAAATTTAGAGAAAATA
Found at i:7639 original size:27 final size:27
Alignment explanation
Indices: 7579--7642 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
7569 TTTATTTGGG
* * *
7579 AAATTAGGAAATTTTGAGAAAATAGGG
1 AAATTGGGAAATTTAGAGAAAATAGGA
*
7606 AAATTGGGAAATTTAGAGAGAATA-GA
1 AAATTGGGAAATTTAGAGAAAATAGGA
7632 AAATTTGGGAA
1 AAA-TTGGGAA
7643 GTTGGCGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (27 bp):
AAATTGGGAAATTTAGAGAAAATAGGA
Found at i:9400 original size:22 final size:22
Alignment explanation
Indices: 9368--9412 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
9358 AACGGTCAAC
9368 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
9390 GGTCAATGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
9412 G
1 G
9413 TCGGGTCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.20, G:0.51, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:9416 original size:4 final size:5
Alignment explanation
Indices: 9375--9419 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
9365 AACGGTCAAC
*
9375 GGTCG GGTCG GGTCG GGTCAAT GGTCG GGTCG GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTC
9420 AGACAATGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 4 0.11
5 27 0.77
7 4 0.11
ACGTcount: A:0.04, C:0.20, G:0.53, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:14911 original size:17 final size:17
Alignment explanation
Indices: 14891--14928 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
14881 GAAAGTCAAC
14891 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
14908 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
14925 GGTC
1 GGTC
14929 GGTCGGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:14988 original size:10 final size:9
Alignment explanation
Indices: 14938--15006 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
14928 CGGTCGGTCG
*
14938 GGTCAGACC
1 GGTCAAACC
*
14947 GGTCAGACC
1 GGTCAAACC
14956 GGTCAAACC
1 GGTCAAACC
*
14965 GGTTCGAACC
1 GG-TCAAACC
14975 GGTCGAAACC
1 GGTC-AAACC
**
14985 GGTCAAAGT
1 GGTCAAACC
14994 GGTCAGAACC
1 GGTCA-AACC
15004 GGT
1 GGT
15007 TGAAAACCAG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
9 29 0.58
10 21 0.42
ACGTcount: A:0.26, C:0.28, G:0.32, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:14988 original size:29 final size:30
Alignment explanation
Indices: 14940--15027 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
14930 GTCGGTCGGG
*
14940 TCAG-ACCGGTC-AGACCGGTCAAACCGGT
1 TCAGAACCGGTCGAAACCGGTCAAACCGGT
**
14968 TC-GAACCGGTCGAAACCGGTCAAAGTGG-
1 TCAGAACCGGTCGAAACCGGTCAAACCGGT
* * *
14996 TCAGAACCGGTTGAAAACCAGTTAAACCGGT
1 TCAGAACCGGTCG-AAACCGGTCAAACCGGT
15027 T
1 T
15028 TCCAGCAGCC
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.02
28 11 0.23
29 22 0.47
30 12 0.26
31 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.17
Consensus pattern (30 bp):
TCAGAACCGGTCGAAACCGGTCAAACCGGT
Found at i:15915 original size:22 final size:23
Alignment explanation
Indices: 15893--15942 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
15883 TTAATACTAA
*
15893 TATTCATTTT-TTATCAAATTAAT
1 TATT-ATTTTATTACCAAATTAAT
*
15916 TATTATTTTATTACCAAAATTATT
1 TATTATTTTATTACC-AAATTAAT
15940 TAT
1 TAT
15943 ATTATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 8 0.35
24 10 0.43
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATTTTATTACCAAATTAAT
Found at i:16326 original size:16 final size:16
Alignment explanation
Indices: 16305--16335 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16295 TCATTTACAG
16305 GTCAGGTTAAAAACAT
1 GTCAGGTTAAAAACAT
*
16321 GTCAGGTTGAAAACA
1 GTCAGGTTAAAAACA
16336 GGTCGGGTAA
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:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (16 bp):
GTCAGGTTAAAAACAT
Found at i:17944 original size:137 final size:138
Alignment explanation
Indices: 17680--18030 Score: 440
Period size: 138 Copynumber: 2.5 Consensus size: 138
17670 GCCCCAAGGC
* * * * *
17680 CCATTTCGATTATTGGATT-AAGTAATTGGTTAAAATTAATTAGGGTTAATTACTAGACCCTAT-
1 CCATTTCGATTATTCGATTCAA-TAATTGGTTAAAATCAATTAGGATTAA-TATTAGAGCCT-TC
* * * * *
17743 ACTTTAGATTAATTTCATATTTATTCATTTAATTTAGGGAATATTCAATTTGGTCCTCGTCTTAA
63 ATTTTAGGTTTATTTCATATTTAGTCATTTAATTTAGGGAATATTCAATTTGGTCCTCGCCTTAA
*
17808 TGTTAA-GGTT
128 TGTCAATGGTT
* *
17818 CCATTTCGATTATTCGATTCAATAATTGATTAAAATCAATTAGGATTAATATTATAGCCTTCATT
1 CCATTTCGATTATTCGATTCAATAATTGGTTAAAATCAATTAGGATTAATATTAGAGCCTTCATT
* * * *
17883 TTAGGTTTATTT-TTACTTTAGTCCTTTAATTTATGGAATATTCAATTTTGTCCTCGCCTTAATG
66 TTAGGTTTATTTCATA-TTTAGTCATTTAATTTAGGGAATATTCAATTTGGTCCTCGCCTTAATG
17947 TCAATGGTT
130 TCAATGGTT
* * *
17956 CCATTTCGATTGTTCGATTCAATAATTGGTTAAAATCTATTAGGATTAATATTAGAGCCTACATA
1 CCATTTCGATTATTCGATTCAATAATTGGTTAAAATCAATTAGGATTAATATTAGAGCCTTCAT-
*
18021 TTCAGGTTTA
65 TTTAGGTTTA
18031 GTCCTCTAGG
Statistics
Matches: 185, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
136 3 0.02
137 66 0.36
138 105 0.57
139 11 0.06
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (138 bp):
CCATTTCGATTATTCGATTCAATAATTGGTTAAAATCAATTAGGATTAATATTAGAGCCTTCATT
TTAGGTTTATTTCATATTTAGTCATTTAATTTAGGGAATATTCAATTTGGTCCTCGCCTTAATGT
CAATGGTT
Found at i:24854 original size:19 final size:20
Alignment explanation
Indices: 24816--24864 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
24806 CTCTAAATCA
* *
24816 TTTTTCAAAATTTCATTTTT
1 TTTTTCAAAATTCCAATTTT
24836 TTTTTCAAAA-TCCAATTTT
1 TTTTTCAAAATTCCAATTTT
**
24855 GCTTTCAAAA
1 TTTTTCAAAA
24865 GAAAATCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTTCAAAATTCCAATTTT
Found at i:30827 original size:22 final size:22
Alignment explanation
Indices: 30795--30836 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
30785 CACTTAGGTC
*
30795 CCTAAACGTTTCCTAATTTTTT
1 CCTAAACGTTTCCCAATTTTTT
*
30817 CCTAAATGTTTCCCAATTTT
1 CCTAAACGTTTCCCAATTTT
30837 ATACTTTAGC
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:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (22 bp):
CCTAAACGTTTCCCAATTTTTT
Found at i:33978 original size:69 final size:69
Alignment explanation
Indices: 33867--33996 Score: 235
Period size: 69 Copynumber: 1.9 Consensus size: 69
33857 AATTCATACT
33867 ACTTGGGGTCCAAGTGGACCGCATATGATAAATGACATGCCATAGCCTACT-AGGAAGGGAGGGA
1 ACTTGGGGTCCAAGTGGACCGCATATGATAAATGACATGCCATAGCCTACTAAGG-AGGGAGGGA
33931 GGGAG
65 GGGAG
*
33936 ACTTGGGGTCCAAGTGGACCGCATATGATACATGACATGCCATAGCCTACTAAGGAGGGAG
1 ACTTGGGGTCCAAGTGGACCGCATATGATAAATGACATGCCATAGCCTACTAAGGAGGGAG
33997 ACTTATGATA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
69 56 0.95
70 3 0.05
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.18
Consensus pattern (69 bp):
ACTTGGGGTCCAAGTGGACCGCATATGATAAATGACATGCCATAGCCTACTAAGGAGGGAGGGAG
GGAG
Found at i:35767 original size:3 final size:3
Alignment explanation
Indices: 35759--35788 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
35749 TAAATATAAA
35759 TAT TAT TAT TAT TAT TACT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
35789 CATATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:35782 original size:13 final size:13
Alignment explanation
Indices: 35759--35794 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
35749 TAAATATAAA
35759 TATTA-TTATTAT
1 TATTACTTATTAT
35771 TATTACTTATTAT
1 TATTACTTATTAT
*
35784 TATTACATATT
1 TATTACTTATT
35795 TTGCAGCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTACTTATTAT
Done.