Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006114.1 Hibiscus syriacus cultivar Beakdansim tig00014490_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: 125832
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4459 original size:11 final size:11
Alignment explanation
Indices: 4445--4480 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
4435 AAAATAGTAA
*
4445 AAAATCAACAT
1 AAAATAAACAT
*
4456 AAAATAAAAAT
1 AAAATAAACAT
4467 AAAATAAACAT
1 AAAATAAACAT
4478 AAA
1 AAA
4481 TACAAGGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAACAT
Found at i:14226 original size:36 final size:36
Alignment explanation
Indices: 14179--14265 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
14169 ACAAAGTTTT
* *
14179 GTTTCACTTGAAACAAATTATATTTCGCTTAAAACA
1 GTTTCTCTTGAAACAAATTATATCTCGCTTAAAACA
* * * * *
14215 GTTTCTCTTGAAATAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTATATCTCGCTTAAAACA
*
14251 ATTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
14266 TAAACCTTTG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTATATCTCGCTTAAAACA
Found at i:14318 original size:22 final size:22
Alignment explanation
Indices: 14293--14354 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
14283 TTCTCTCGAA
14293 ACAAAGTTTTGTCTTGCTTGAG
1 ACAAAGTTTTGTCTTGCTTGAG
*
14315 AC-AA---TT-T-TT-CTTGAA
1 ACAAAGTTTTGTCTTGCTTGAG
*
14330 ACAAAGTTTTGTCTCGCTTGAG
1 ACAAAGTTTTGTCTTGCTTGAG
14352 ACA
1 ACA
14355 GTTTCTCTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 1 0.03
18 2 0.07
19 2 0.07
20 1 0.03
21 3 0.10
22 10 0.33
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (22 bp):
ACAAAGTTTTGTCTTGCTTGAG
Found at i:14331 original size:37 final size:37
Alignment explanation
Indices: 14282--14369 Score: 140
Period size: 37 Copynumber: 2.4 Consensus size: 37
14272 TTTGAGATTG
* *
14282 TTTCTCTCGAAACAAAGTTTTGTCTTGCTTGAGACAA
1 TTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAA
* *
14319 TTTTTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAA
14356 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
14370 TGAACCTCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAA
Found at i:14360 original size:104 final size:103
Alignment explanation
Indices: 14216--14436 Score: 343
Period size: 104 Copynumber: 2.1 Consensus size: 103
14206 CTTAAAACAG
* *
14216 TTTCTCTTGAAATAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGATT
1 TTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTCTGAGATT
*
14281 GTTTCTCTCGAAACAAAGTTTTGTCTTGCTTGAGACAA
66 GTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAA
* * *
14319 TTTTTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATGAACCTCTGAGAT
1 TTTCTCTTGAAACAAA-TTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTCTGAGAT
* * * *
14384 TGTTTCTCTTGAAACAAAGTTTTGTGTCGCTTGAGATAG
65 TGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAA
14423 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
14437 TAAACCTTTG
Statistics
Matches: 106, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
103 14 0.13
104 92 0.87
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (103 bp):
TTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTCTGAGATT
GTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAA
Found at i:14382 original size:67 final size:67
Alignment explanation
Indices: 14318--14569 Score: 267
Period size: 67 Copynumber: 3.8 Consensus size: 67
14308 GCTTGAGACA
* * *
14318 ATTTTTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATGAACCTCTGAGA
1 ATTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTCTGAGA
14383 TT
66 TT
* * *
14385 GTTTCTCTTGAAACAAAGTTTTGTGTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
1 ATTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTCTGAGA
14450 TT
66 TT
* * * ** *
14452 ATTTCTCTAGAAACAAAGTTTCGTCTC-CTTTGAGATAGTTTTCCCTTGAAATGTAAA-TTCT-A
1 ATTTCTCTTGAAACAAAGTTTTGTCTCGC-TTGAGATAG-TTTCTCTTGAAACATAAACCTCTGA
*
14514 AATT
64 GATT
* * * * * ** * *
14518 GTTTCACTCGAAACAAATTTTTATCTTACATGAGATAGCTTCTCTTGAAACA
1 ATTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACA
14570 AATTTCTTTC
Statistics
Matches: 154, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
65 10 0.06
66 33 0.21
67 96 0.62
68 15 0.10
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (67 bp):
ATTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTCTGAGA
TT
Found at i:14981 original size:140 final size:140
Alignment explanation
Indices: 14669--15321 Score: 794
Period size: 140 Copynumber: 4.7 Consensus size: 140
14659 AAGTCAATCA
* * * * *
14669 TCATCAACCGACCATATCTCCTCAACGCGTAGGAGTAGCGTCATCCTCAGATAACCATACTTCCT
1 TCATCCACCGACCATATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCATACTTCCT
* * * *
14734 CATCACATAGGAACCATGTTGTCT-CTAAATTATCCCTAAAGACGGCTAGACATCCTCATCACGT
66 CATCACGTAGGAACCATGTTGTCTCCAAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGT
14798 AGGAACAATG
131 AGGAACAATG
* * ** * *
14808 TCATCCACCGACCAGATCTCCTCAACGTGTAGGAGCAGTGTCATCCTTTA-ATAACCAGACTTCC
1 TCATCCACCGACCATATCTCCTCATCACGTAGGAGCAGCGTCATCC-TTAGATAACCATACTTCC
* *
14872 TTATCACGTAGGAACCATGTTGTCTCCAAAATTATCCCTACAGATGGCTAGACGTCCTCATCACG
65 TCATCACGTAGGAACCATGTTGTCTCCAAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACG
14937 TAGGAACAATG
130 TAGGAACAATG
* * * * * * * * * *
14948 TCGTCCACAGACGATATCTCCTCATCACATAGGAGAAGCATCATTCTCAGATAACCAGACTTTCT
1 TCATCCACCGACCATATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCATACTTCCT
* * * * *
15013 CATCACGTAGG-ACTCGA-GTTGTCTCCCAAATTATCCTTAAATATGACTAGACTTCCTCATCAC
66 CATCACGTAGGAAC-C-ATGTTGTCTCCAAAATTATCCCTAAAGATGGCTAGACGTCCTCATCAC
15076 GTAGGAACAATG
129 GTAGGAACAATG
* * * * *
15088 TCGTCCATCGACCATATCTCCTCATCACGTAAGAGCAGCGTCAT-TTTCAGATAACCATACTTCT
1 TCATCCACCGACCATATCTCCTCATCACGTAGGAGCAGCGTCATCCTT-AGATAACCATACTTCC
* * * *
15152 TCATCACGTAGGAACCGTGTTGTCTCCCAAATTATCCCTAAAGATGGCTAGATGTCCTAATCACG
65 TCATCACGTAGGAACCATGTTGTCTCCAAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACG
*
15217 TATGAACAATG
130 TAGGAACAATG
* * * * * *
15228 TCATCCACCGACCAGATCTCCTCATCATGTAAGAGCAGTGTCATTCTTAGATAACCATATTTCCT
1 TCATCCACCGACCATATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCATACTTCCT
*
15293 CATCACGTAGGAACCGTGTTGTCTCCAAA
66 CATCACGTAGGAACCATGTTGTCTCCAAA
15322 TTTACCTAAA
Statistics
Matches: 442, Mismatches: 63, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
139 82 0.19
140 355 0.80
141 5 0.01
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (140 bp):
TCATCCACCGACCATATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCATACTTCCT
CATCACGTAGGAACCATGTTGTCTCCAAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGT
AGGAACAATG
Found at i:15494 original size:3 final size:3
Alignment explanation
Indices: 15486--15559 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
15476 GGATGAGTAG
15486 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
15534 CTA CTA CTA CTA CTA CTA CTA CTA CT
1 CTA CTA CTA CTA CTA CTA CTA CTA CT
15560 TTAACAATAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
CTA
Found at i:22036 original size:19 final size:19
Alignment explanation
Indices: 22012--22052 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
22002 ACAAAGGACA
22012 GGGGGTTCACGAGCAAAAG
1 GGGGGTTCACGAGCAAAAG
22031 GGGGGTTCACGAGCAAAAG
1 GGGGGTTCACGAGCAAAAG
22050 GGG
1 GGG
22053 AAATTGACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.15, G:0.46, T:0.10
Consensus pattern (19 bp):
GGGGGTTCACGAGCAAAAG
Found at i:25234 original size:2 final size:2
Alignment explanation
Indices: 25227--25263 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25217 ATAAAAATTA
25227 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 A
25264 AAACCATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27129 original size:31 final size:31
Alignment explanation
Indices: 27091--27254 Score: 256
Period size: 31 Copynumber: 5.3 Consensus size: 31
27081 TTTAATTTTA
* *
27091 TCAATTATAACATTGAACTTTGATTTTCTTT
1 TCAATTATAGCATTGAACTTTGATTTTCGTT
* *
27122 TCAATTATAGCATAGAACTTTGATTTCCGTT
1 TCAATTATAGCATTGAACTTTGATTTTCGTT
27153 TCAATTATAGCATTGAACTTTGATTTTCGTT
1 TCAATTATAGCATTGAACTTTGATTTTCGTT
* * *
27184 TCATTTATAGTATTGGACTTTGATTTTCGTT
1 TCAATTATAGCATTGAACTTTGATTTTCGTT
*
27215 TCAATTATAGCATTAAACTTTGATTTTCGTT
1 TCAATTATAGCATTGAACTTTGATTTTCGTT
27246 TCAATTATA
1 TCAATTATA
27255 CTAATAGGTC
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 120 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (31 bp):
TCAATTATAGCATTGAACTTTGATTTTCGTT
Found at i:31663 original size:61 final size:61
Alignment explanation
Indices: 31568--31690 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
31558 GCAGACACTC
*
31568 CCTGGAAAACAATTAACATTTGTTTAATTTTGTTCCCTGATAATCAAATTGTTACATGCGA
1 CCTGGAAAACAATTAACATTTGTTTAATTTTGTTCCCTGATAATCAAATTGGTACATGCGA
*
31629 CCTGGAAAACAATTATCATTTGTTTAATTTTGTTCCCTGATAATCAAATTGGTACATGCGA
1 CCTGGAAAACAATTAACATTTGTTTAATTTTGTTCCCTGATAATCAAATTGGTACATGCGA
31690 C
1 C
31691 TTAGAGTCAC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (61 bp):
CCTGGAAAACAATTAACATTTGTTTAATTTTGTTCCCTGATAATCAAATTGGTACATGCGA
Found at i:32309 original size:17 final size:17
Alignment explanation
Indices: 32287--32320 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
32277 GATTTGCATC
32287 TTCAAATGTTCTTCCTT
1 TTCAAATGTTCTTCCTT
32304 TTCAAATGTTCTTCCTT
1 TTCAAATGTTCTTCCTT
32321 AAGCATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.53
Consensus pattern (17 bp):
TTCAAATGTTCTTCCTT
Found at i:32777 original size:11 final size:12
Alignment explanation
Indices: 32757--32789 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
32747 TTGCGAGGCA
32757 AAAAATAAAAAG
1 AAAAATAAAAAG
32769 AAAAA-AAAAAG
1 AAAAATAAAAAG
32780 ACAAAATAAA
1 A-AAAATAAA
32790 CAGATTGCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.37
12 9 0.47
13 3 0.16
ACGTcount: A:0.85, C:0.03, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAATAAAAAG
Found at i:36373 original size:26 final size:26
Alignment explanation
Indices: 36344--36422 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
36334 GGTCTGATGT
36344 GGCAGTTTCTAAAAGGTCCAGTCAGC
1 GGCAGTTTCTAAAAGGTCCAGTCAGC
* *
36370 GGCAGTTTCTAAAAAGTCCAGTCAGT
1 GGCAGTTTCTAAAAGGTCCAGTCAGC
* * * *
36396 GACAGTTTCTAGAAGATCTAGTCAGC
1 GGCAGTTTCTAAAAGGTCCAGTCAGC
36422 G
1 G
36423 CGCCTTCTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (26 bp):
GGCAGTTTCTAAAAGGTCCAGTCAGC
Found at i:40052 original size:17 final size:17
Alignment explanation
Indices: 40026--40081 Score: 94
Period size: 17 Copynumber: 3.3 Consensus size: 17
40016 TGCACAAAAT
*
40026 TAAAATCGAAGAAGGCG
1 TAAAACCGAAGAAGGCG
*
40043 TAAAACCGAAGAAGGTG
1 TAAAACCGAAGAAGGCG
40060 TAAAACCGAAGAAGGCG
1 TAAAACCGAAGAAGGCG
40077 TAAAA
1 TAAAA
40082 TCGACACGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.50, C:0.12, G:0.27, T:0.11
Consensus pattern (17 bp):
TAAAACCGAAGAAGGCG
Found at i:42208 original size:6 final size:6
Alignment explanation
Indices: 42198--42233 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
42188 ATTCCGTTAC
*
42198 ATTTTC ATTTTCA ATTTTA ATTTTA ATTTTA ATTTT
1 ATTTTA ATTTT-A ATTTTA ATTTTA ATTTTA ATTTT
42234 GATTAAGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:45388 original size:17 final size:17
Alignment explanation
Indices: 45366--45406 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
45356 AAAAGACGTG
45366 AAAAAATG-GAAAACAAA
1 AAAAAATGTGAAAA-AAA
*
45383 AAAAAATGTGAAAAAGA
1 AAAAAATGTGAAAAAAA
45400 AAAAAAT
1 AAAAAAT
45407 CAAATGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (17 bp):
AAAAAATGTGAAAAAAA
Found at i:46231 original size:26 final size:26
Alignment explanation
Indices: 46157--46220 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
46147 GTCTAACGTG
46157 GCAGTTTCTAGATGGTCCAGTCAACA
1 GCAGTTTCTAGATGGTCCAGTCAACA
46183 GCAGTTTCTAGATGGTCCAGTCAACA
1 GCAGTTTCTAGATGGTCCAGTCAACA
46209 GCAGTTTCTAGA
1 GCAGTTTCTAGA
46221 AGAGCTAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (26 bp):
GCAGTTTCTAGATGGTCCAGTCAACA
Found at i:48123 original size:17 final size:16
Alignment explanation
Indices: 48103--48149 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
48093 AATATTTTTA
48103 AAAAATCAATAAATTT
1 AAAAATCAATAAATTT
*
48119 GAAAACA-CAATATGATTT
1 -AAAA-ATCAATA-AATTT
48137 AAAAATCAATAAA
1 AAAAATCAATAAA
48150 CCTGATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
16 2 0.08
17 18 0.72
18 5 0.20
ACGTcount: A:0.62, C:0.09, G:0.04, T:0.26
Consensus pattern (16 bp):
AAAAATCAATAAATTT
Found at i:48361 original size:23 final size:24
Alignment explanation
Indices: 48335--48391 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
48325 ATATATACAT
** *
48335 TAAAAATATA-TTCTATACGATAA
1 TAAAAATATACTAATATAAGATAA
*
48358 TAAAATTATACGTAATATAAGATAA
1 TAAAAATATAC-TAATATAAGATAA
48383 TAAAAATAT
1 TAAAAATAT
48392 TATATATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 9 0.33
25 18 0.67
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (24 bp):
TAAAAATATACTAATATAAGATAA
Found at i:48444 original size:2 final size:2
Alignment explanation
Indices: 48388--48432 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
48378 GATAATAAAA
48388 AT AT -T AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
48429 AT AT
1 AT AT
48433 CATGTAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:64068 original size:30 final size:31
Alignment explanation
Indices: 64034--64100 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
64024 TACAACACCT
64034 AACTTTT-GAAAATTA-CACTTTTGGTCCCTA
1 AACTTTTAGAAAATTATC-CTTTTGGTCCCTA
*
64064 AACTTTTAGAAATTTATCCTTTTGGTCCCTA
1 AACTTTTAGAAAATTATCCTTTTGGTCCCTA
64095 AACTTT
1 AACTTT
64101 CCAAACTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 7 0.21
31 26 0.76
32 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.43
Consensus pattern (31 bp):
AACTTTTAGAAAATTATCCTTTTGGTCCCTA
Found at i:64111 original size:31 final size:29
Alignment explanation
Indices: 64051--64148 Score: 103
Period size: 31 Copynumber: 3.3 Consensus size: 29
64041 GAAAATTACA
*
64051 CTTTTGGTCCCTAAACTTTTAGAAATTTAT
1 CTTTTGGTCCCTAAACTTTCA-AAATTTAT
*
64081 CCTTTTGGTCCCTAAACTTTCCAAACTTTAT
1 -CTTTTGGTCCCTAAACTTT-CAAAATTTAT
64112 AC-TTTGG-CCACTAAA-TTTCAAAATTTAT
1 -CTTTTGGTCC-CTAAACTTTCAAAATTTAT
*
64140 ATTTTGGTC
1 CTTTTGGTC
64149 AATAACTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
28 14 0.24
29 6 0.10
30 10 0.17
31 27 0.47
32 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (29 bp):
CTTTTGGTCCCTAAACTTTCAAAATTTAT
Found at i:67748 original size:14 final size:14
Alignment explanation
Indices: 67729--67775 Score: 94
Period size: 14 Copynumber: 3.4 Consensus size: 14
67719 GAGTCAAATA
67729 TTGTACTGTAGTGC
1 TTGTACTGTAGTGC
67743 TTGTACTGTAGTGC
1 TTGTACTGTAGTGC
67757 TTGTACTGTAGTGC
1 TTGTACTGTAGTGC
67771 TTGTA
1 TTGTA
67776 GATAAGGTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.15, C:0.13, G:0.28, T:0.45
Consensus pattern (14 bp):
TTGTACTGTAGTGC
Found at i:71671 original size:57 final size:57
Alignment explanation
Indices: 71602--71720 Score: 229
Period size: 57 Copynumber: 2.1 Consensus size: 57
71592 AATATCTAGT
*
71602 ACGAATTAGCGAATTGAGAAGTGGGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
1 ACGAATTAGCGAATTGAGAAGTGAGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
71659 ACGAATTAGCGAATTGAGAAGTGAGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
1 ACGAATTAGCGAATTGAGAAGTGAGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
71716 ACGAA
1 ACGAA
71721 GGGCTGCCGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.24
Consensus pattern (57 bp):
ACGAATTAGCGAATTGAGAAGTGAGATTTAGCTCGAATATGGGGGCTGTCAGATCGA
Found at i:74358 original size:32 final size:32
Alignment explanation
Indices: 74291--74351 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
74281 TGACATGGAT
* *
74291 TATGTCATATCATTACTTTAAGTGATGTTCTA
1 TATGTCATATCATCACTTTAAGTGATGTGCTA
**
74323 TATGTCATATCATCACTTTGGGTGATGTG
1 TATGTCATATCATCACTTTAAGTGATGTG
74352 GCATATGCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (32 bp):
TATGTCATATCATCACTTTAAGTGATGTGCTA
Found at i:79315 original size:77 final size:78
Alignment explanation
Indices: 79206--79359 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 78
79196 ATAGGAAAGA
*
79206 TGATGGAACTCTAGGAAAACTTAGGTTATAGAAAATCTCTAGTTTTTCCATACTAATTCAAAGAT
1 TGATGGAACTCAAGGAAAACTTAGGTTATAGAAAATCTCTAGTTTTTCCATACTAATTCAAAGAT
79271 AATAATGAGATAT
66 AATAATGAGATAT
*
79284 TGATGGAACTCAAGG-AAACTTAGGTTATAGAAAATCTCTAGTTTTTCCATATTAATTCAAAGAT
1 TGATGGAACTCAAGGAAAACTTAGGTTATAGAAAATCTCTAGTTTTTCCATACTAATTCAAAGAT
79348 AATAATGAGATA
66 AATAATGAGATA
79360 GATATGTTGG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 60 0.81
78 14 0.19
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (78 bp):
TGATGGAACTCAAGGAAAACTTAGGTTATAGAAAATCTCTAGTTTTTCCATACTAATTCAAAGAT
AATAATGAGATAT
Found at i:83382 original size:15 final size:15
Alignment explanation
Indices: 83362--83395 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
83352 TTGCAGTCTC
83362 CGGCATTCAGTATTT
1 CGGCATTCAGTATTT
83377 CGGCATTCAGTATTT
1 CGGCATTCAGTATTT
83392 CGGC
1 CGGC
83396 TTAGGAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (15 bp):
CGGCATTCAGTATTT
Found at i:84876 original size:23 final size:23
Alignment explanation
Indices: 84850--84905 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
84840 ATTAATAAAA
84850 ATATATTAAA-TTATTTTT-TATTC
1 ATATA-TAAATTTATTTTTATA-TC
*
84873 ATATATATATTTATTTTTATATC
1 ATATATAAATTTATTTTTATATC
84896 ATATAATAAA
1 ATAT-ATAAA
84906 ACATAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 19 0.68
24 6 0.21
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATATAAATTTATTTTTATATC
Found at i:97914 original size:21 final size:22
Alignment explanation
Indices: 97879--97959 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
97869 TTGGTGCAGA
*
97879 GGGAATCGA-TCCCCCCATCA-
1 GGGAACCGATTCCCCCCATCAG
** *
97899 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCAT-CAG
97922 GGGAACCGATTCCCCCCA-CAG
1 GGGAACCGATTCCCCCCATCAG
* *
97943 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
97960 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 8 0.16
21 24 0.49
22 1 0.02
23 16 0.33
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCATCAG
Found at i:100237 original size:12 final size:12
Alignment explanation
Indices: 100220--100244 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
100210 ACATGATAAA
100220 TTGAAGAAGTGT
1 TTGAAGAAGTGT
100232 TTGAAGAAGTGT
1 TTGAAGAAGTGT
100244 T
1 T
100245 AAAGTAAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (12 bp):
TTGAAGAAGTGT
Found at i:106657 original size:19 final size:18
Alignment explanation
Indices: 106633--106681 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
106623 AGGCAAAAAC
*
106633 AAAAAGAAAAAAAAAGTGA
1 AAAAAGAAAAAAAAA-TAA
*
106652 AAAAAGAAGAAAAAATAA
1 AAAAAGAAAAAAAAATAA
106670 AAGAAAGAAAAA
1 AA-AAAGAAAAA
106682 TGATCAAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAAAAATAA
Found at i:109951 original size:137 final size:137
Alignment explanation
Indices: 109679--109944 Score: 327
Period size: 137 Copynumber: 1.9 Consensus size: 137
109669 TAATGTTATC
* * * * * *
109679 TCCAAATACGACTATACGTCCTCAATACGAAAGAACAATGTCGTCCACCGACCAGATCTCTTCTA
1 TCCAAATACGACTAGACGTCCTCAACACGAAAGAACAATGTCGTCCACCAACCAAATCTCCTCAA
* * * * * * *
109744 TGCGAAGGAGTAGTGTTATCCTCAGACAATCAGACTTCCTCAACACAAAAGAATCTTGTTGTCTC
66 TACGAAGGAGCAGTGTCATCCTCACACAATCAGACTTCCTCAACACAAAAGAACCATGTTATCTC
109809 CAAATTA
131 CAAATTA
* * * *
109816 TCCAAATATGTCTAGACGTCCTCAACACGAAGGACCAATG-CTGTCCACCAACCAAATCTCCTCA
1 TCCAAATACGACTAGACGTCCTCAACACGAAAGAACAATGTC-GTCCACCAACCAAATCTCCTCA
* * * *
109880 ATACGAAGGAGCAGTGTCATCCTCTCACAATCAGACTTCCTCAACGCGAAGGAACCATGTTATCT
65 ATACGAAGGAGCAGTGTCATCCTCACACAATCAGACTTCCTCAACACAAAAGAACCATGTTATCT
109945 TTAAATTGCC
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
136 1 0.01
137 106 0.99
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.24
Consensus pattern (137 bp):
TCCAAATACGACTAGACGTCCTCAACACGAAAGAACAATGTCGTCCACCAACCAAATCTCCTCAA
TACGAAGGAGCAGTGTCATCCTCACACAATCAGACTTCCTCAACACAAAAGAACCATGTTATCTC
CAAATTA
Found at i:110347 original size:3 final size:3
Alignment explanation
Indices: 110328--110379 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
110318 CCGAGTTTTA
* * * *
110328 ATT ATTT ATT GTT ATT ATT ATT TTT ATTT ATT ATT ACT ACT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
110375 ATT AT
1 ATT AT
110380 AAATAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:110357 original size:22 final size:22
Alignment explanation
Indices: 110328--110377 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
110318 CCGAGTTTTA
* * *
110328 ATTATTTATTGTTATTATTATT
1 ATTATTTATTATTACTACTATT
*
110350 TTTATTTATTATTACTACTATT
1 ATTATTTATTATTACTACTATT
110372 ATTATT
1 ATTATT
110378 ATAAATAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTATTTATTATTACTACTATT
Found at i:113687 original size:15 final size:15
Alignment explanation
Indices: 113664--113714 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
113654 GATATTAGTT
* *
113664 GGGCAGGCGGATGTG
1 GGGCGGGCGGATGCG
113679 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
* *
113694 GGACGGGTGGATGCG
1 GGGCGGGCGGATGCG
*
113709 GTGCGG
1 GGGCGG
113715 ATGCAGGGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.10, C:0.16, G:0.63, T:0.12
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:114070 original size:43 final size:43
Alignment explanation
Indices: 114035--114118 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
114025 TCTAAACCGT
114035 CACTAAAAACCCTAACCTTTTACGGTGTTTGTGTCTAAAAAAC
1 CACTAAAAACCCTAACCTTTTACGGTGTTTGTGTCTAAAAAAC
*
114078 CACTAAAAACCCTAACCTTTTATGGTGTTTGTAGT-TAAAAA
1 CACTAAAAACCCTAACCTTTTACGGTGTTTGT-GTCTAAAAA
114119 CACCTCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 37 0.95
44 2 0.05
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (43 bp):
CACTAAAAACCCTAACCTTTTACGGTGTTTGTGTCTAAAAAAC
Found at i:115228 original size:35 final size:35
Alignment explanation
Indices: 115189--115259 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
115179 GATTACATAC
* *
115189 ATCGAGACGAAAATATTT-TTAAGACAGTGGTTTAT
1 ATCGAGACGAAAATATTTCTAAAG-CAATGGTTTAT
*
115224 ATCGAGACGAAACTATTTCTAAAGCAATGGTTTAT
1 ATCGAGACGAAAATATTTCTAAAGCAATGGTTTAT
115259 A
1 A
115260 CCACACCACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (35 bp):
ATCGAGACGAAAATATTTCTAAAGCAATGGTTTAT
Found at i:119279 original size:41 final size:42
Alignment explanation
Indices: 119233--119324 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
119223 TGACGGATAG
** *
119233 CCCTAAGGACTT-ATTATCTTGCTCAAAAGACTGACAGATGA
1 CCCTAAGGACTTAAGCATCATGCTCAAAAGACTGACAGATGA
* * *
119274 CCCTAATGATTTAAGCATCATGCTCGAAAGACTGACAGATGA
1 CCCTAAGGACTTAAGCATCATGCTCAAAAGACTGACAGATGA
*
119316 CCCGAAGGA
1 CCCTAAGGA
119325 TTTACAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 10 0.24
42 32 0.76
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (42 bp):
CCCTAAGGACTTAAGCATCATGCTCAAAAGACTGACAGATGA
Done.