Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005011.1 Hibiscus syriacus cultivar Beakdansim tig00011248_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: 61542
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:11513 original size:18 final size:19
Alignment explanation
Indices: 11489--11536 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
11479 GGAATTTGAA
*
11489 ATTAGGATTATCTATTGTT
1 ATTAGGATTATCTATTATT
* *
11508 -TTAGGAATTTTCTTTTATT
1 ATTAGG-ATTATCTATTATT
11527 ATTAGGATTA
1 ATTAGGATTA
11537 AGTTTGAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.54
Consensus pattern (19 bp):
ATTAGGATTATCTATTATT
Found at i:12369 original size:23 final size:23
Alignment explanation
Indices: 12310--12372 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
12300 AGCATTTTCA
*
12310 TCTTTATTTCCTTTAAAGTAATT
1 TCTTTATTTACTTTAAAGTAATT
* * * *
12333 TCTTTGTTTTCTTTAGATTAAATT
1 TCTTTATTTACTTTAAAGT-AATT
12357 T-TTTATTTACTTTAAA
1 TCTTTATTTACTTTAAA
12373 AACTTCTCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 27 0.84
24 5 0.16
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (23 bp):
TCTTTATTTACTTTAAAGTAATT
Found at i:24202 original size:24 final size:25
Alignment explanation
Indices: 24175--24222 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
24165 GCCTATTTTT
* * *
24175 GATGAGGAACCTGAA-ACAATGCAA
1 GATGAAGAAACTGAAGAAAATGCAA
24199 GATGAAGAAACTGAAGAAAATGCA
1 GATGAAGAAACTGAAGAAAATGCA
24223 GATCATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (25 bp):
GATGAAGAAACTGAAGAAAATGCAA
Found at i:32249 original size:8 final size:8
Alignment explanation
Indices: 32236--32304 Score: 72
Period size: 8 Copynumber: 9.0 Consensus size: 8
32226 TATTTTTTTT
32236 CAAAAAAA
1 CAAAAAAA
32244 C-AAAAAA
1 CAAAAAAA
32251 CAAAAAAA
1 CAAAAAAA
32259 CAAAAAAA
1 CAAAAAAA
***
32267 GGCAAAAA
1 CAAAAAAA
32275 -AAAAAAA
1 CAAAAAAA
**
32282 C-AAAAGG
1 CAAAAAAA
32289 CAAAAAAA
1 CAAAAAAA
32297 CAAAAAAA
1 CAAAAAAA
32305 GAGCCAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
7 17 0.35
8 32 0.65
ACGTcount: A:0.83, C:0.12, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:32256 original size:15 final size:15
Alignment explanation
Indices: 32238--32303 Score: 66
Period size: 15 Copynumber: 4.4 Consensus size: 15
32228 TTTTTTTTCA
32238 AAAAAAC-AAAAAAC
1 AAAAAACAAAAAAAC
32252 AAAAAAACAAAAAAAGGC
1 -AAAAAACAAAAAAA--C
32270 -AAAAA-AAAAAAAC
1 AAAAAACAAAAAAAC
**
32283 AAAAGGCAAAAAAAC
1 AAAAAACAAAAAAAC
32298 AAAAAA
1 AAAAAA
32304 AGAGCCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 1 0.02
14 3 0.07
15 26 0.62
16 11 0.26
18 1 0.02
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAAAAAC
Found at i:32275 original size:20 final size:19
Alignment explanation
Indices: 32237--32315 Score: 87
Period size: 19 Copynumber: 4.3 Consensus size: 19
32227 ATTTTTTTTC
32237 AAAAAAAC-AAAAAA--C-
1 AAAAAAACAAAAAAAGGCA
32252 AAAAAAACAAAAAAAGGCA
1 AAAAAAACAAAAAAAGGCA
*
32271 AAAAAAAAAAACAAAAGGC-
1 AAAAAAACAAA-AAAAGGCA
32290 AAAAAAACAAAAAAAGAGCCA
1 AAAAAAACAAAAAAAG-G-CA
32311 AAAAA
1 AAAAA
32316 GCCAAAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
15 8 0.15
16 6 0.11
18 6 0.11
19 21 0.39
20 8 0.15
21 5 0.09
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAGGCA
Found at i:32284 original size:38 final size:39
Alignment explanation
Indices: 32237--32315 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 39
32227 ATTTTTTTTC
32237 AAAAAAACAAAAAACAAAAAAACAAAAAAAG-GCAAAAA
1 AAAAAAACAAAAAACAAAAAAACAAAAAAAGAGCAAAAA
** *
32275 AAAAAAACAAAAGGCAAAAAAACAAAAAAAGAGCCAAAA
1 AAAAAAACAAAAAACAAAAAAACAAAAAAAGAGCAAAAA
32314 AA
1 AA
32316 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 29 0.78
39 8 0.22
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (39 bp):
AAAAAAACAAAAAACAAAAAAACAAAAAAAGAGCAAAAA
Found at i:37045 original size:15 final size:15
Alignment explanation
Indices: 37025--37063 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
37015 GGCATGGATA
* *
37025 ATAATGGTGATGGTG
1 ATAATGATGATGATG
37040 ATAATGATGATGATG
1 ATAATGATGATGATG
*
37055 ATAGTGATG
1 ATAATGATG
37064 GTGGTGGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (15 bp):
ATAATGATGATGATG
Found at i:41103 original size:10 final size:10
Alignment explanation
Indices: 41090--41115 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41080 AAACTCTTCA
41090 TCCTTCTTAT
1 TCCTTCTTAT
41100 TCCTTCTTAT
1 TCCTTCTTAT
41110 TCCTTC
1 TCCTTC
41116 ATCCGTGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.35, G:0.00, T:0.58
Consensus pattern (10 bp):
TCCTTCTTAT
Found at i:41399 original size:34 final size:34
Alignment explanation
Indices: 41361--41430 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
41351 AGTATAAAGT
41361 GTTAGAAATGAAATTAGATCATGTTGGAAATTTA
1 GTTAGAAATGAAATTAGATCATGTTGGAAATTTA
41395 GTTAGAAATGAAATTAGATCATGTTGGAAATTTA
1 GTTAGAAATGAAATTAGATCATGTTGGAAATTTA
41429 GT
1 GT
41431 AAGATTCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (34 bp):
GTTAGAAATGAAATTAGATCATGTTGGAAATTTA
Found at i:41795 original size:34 final size:34
Alignment explanation
Indices: 41730--41798 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
41720 ATCCTTCACA
*
41730 GGGTATCGATACCGAAGTGGTAGTATTGGTACCAT
1 GGGTATCGATACCGAAG-GGTAGTATCGGTACCAT
41765 GGGTATCGATACCGATA-GGTAGTATCGGTACCAT
1 GGGTATCGATACCGA-AGGGTAGTATCGGTACCAT
41799 TTTTAGAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 16 0.50
35 15 0.47
36 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (34 bp):
GGGTATCGATACCGAAGGGTAGTATCGGTACCAT
Found at i:43319 original size:24 final size:24
Alignment explanation
Indices: 43287--43341 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
43277 AAACCGCATT
43287 GACAACACGTATGAAGATGTCCCA
1 GACAACACGTATGAAGATGTCCCA
43311 GACAACACGTATGAAGATGTCCCA
1 GACAACACGTATGAAGATGTCCCA
43335 GACAACA
1 GACAACA
43342 TCAAAATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (24 bp):
GACAACACGTATGAAGATGTCCCA
Found at i:47531 original size:15 final size:15
Alignment explanation
Indices: 47511--47549 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
47501 TCGCTTGATT
47511 TTGCTTCGATTACGA
1 TTGCTTCGATTACGA
*
47526 TTGCTTCGATTATGA
1 TTGCTTCGATTACGA
*
47541 TTGCCTCGA
1 TTGCTTCGA
47550 ACATTGGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (15 bp):
TTGCTTCGATTACGA
Found at i:48514 original size:20 final size:21
Alignment explanation
Indices: 48469--48519 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
48459 TTCAGTTTAA
* *
48469 AATTTATAGAATTAAATAATTG
1 AATTTAT-GAACTAAACAATTG
48491 -ATTTATGAACTAAACAA-TG
1 AATTTATGAACTAAACAATTG
*
48510 AATTTCTGAA
1 AATTTATGAA
48520 ACTTTTAGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 17 0.68
21 6 0.24
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (21 bp):
AATTTATGAACTAAACAATTG
Found at i:54005 original size:19 final size:19
Alignment explanation
Indices: 53981--54018 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
53971 TTTGGGCATG
53981 ATGTTTTTATATGATATTT
1 ATGTTTTTATATGATATTT
54000 ATGTTTTTATATGATATTT
1 ATGTTTTTATATGATATTT
54019 TTTTAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (19 bp):
ATGTTTTTATATGATATTT
Found at i:57220 original size:81 final size:80
Alignment explanation
Indices: 56986--57842 Score: 1067
Period size: 81 Copynumber: 10.7 Consensus size: 80
56976 GCATATAGCT
* * * *
56986 TTTCATCTAACTTGCATGATTGACAACTTCCTGTCAAATGCACAGCTAGGCCATTAATATTTGAC
1 TTTCATCTAACTTGCATAATTGAC-ACTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
57051 TCAAAGGTATTTAACC
65 TCAAAGGTATTTAACC
** * * * *
57067 TTTCATCTAACTAACATAATTGATACATTCTGTCAAATGCATAACTAGGCCATTAATCTTTTACT
1 TTTCATCTAACTTGCATAATTGACACTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTACT
*
57132 CAAAGGTATTTAACG
66 CAAAGGTATTTAACC
** * * *
57147 TTTCATCTAACTTGCATAATTGACATCTTTCTGTCAGTTGCATAGGC-AAGCCATTAATATTTTA
1 TTTCATCTAACTTGCATAATTGACA-CTTTCTGTCAAATGCACA-ACTAGGCCATTAATATTTTA
57211 CTCAAAGGTATTTAACC
64 CTCAAAGGTATTTAACC
* * *
57228 TTTCATCTAACTGGTATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATATTTTAC
1 TTTCATCTAACTTGCATAATTGACAC-TTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
**
57293 TCAAATATATTTAACC
65 TCAAAGGTATTTAACC
* *
57309 -TTCATCTAA-TTGGCATAATTGACACCTTTATGTCAAATGCACATCTAGGCCATTAATATTTTA
1 TTTCATCTAACTT-GCATAATTGACA-CTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTA
57372 CTCAAAGGTATTTAACC
64 CTCAAAGGTATTTAACC
* * * * * *
57389 TTTCATATAACTGGCAT-A-T-ACACCTTTCTATCAAATGCACAA-T----TATTAATCTTTTAG
1 TTTCATCTAACTTGCATAATTGACA-CTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
*
57446 TGAAAGGTATTTAACC
65 TCAAAGGTATTTAACC
* *
57462 TTTCATCTAA-TTGGCATAATTAACACTTTTCTGTCAAATGCACAACTAGGCCAGTAATATTTTA
1 TTTCATCTAACTT-GCATAATTGACAC-TTTCTGTCAAATGCACAACTAGGCCATTAATATTTTA
57526 CTCAAAGGTATTTAACC
64 CTCAAAGGTATTTAACC
* * * * * * *
57543 TTTCATCTAACTAGAATAATTGACACAGTTCTGTCAATTGCACAGCTAGACCATTAAT-CTTTAC
1 TTTCATCTAACTTGCATAATTGACAC-TTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
*
57607 TCAAAGGCATTTAACC
65 TCAAAGGTATTTAACC
* *
57623 TTTCATCTAA-TTGGCATAATTGACACATTTCTATCAAATGCACAACTAGGCCATTAATCTTTTA
1 TTTCATCTAACTT-GCATAATTGACAC-TTTCTGTCAAATGCACAACTAGGCCATTAATATTTTA
* *
57687 CTCAAAGATATTGAACC
64 CTCAAAGGTATTTAACC
*
57704 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
1 TTTCATCTAACTTGCATAATTGACA-CTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
57769 TCAAAGGTATTTAACC
65 TCAAAGGTATTTAACC
* *
57785 TTTCATCTAACTGGCATAATTGACACATTTCTTTCAAATGCACAACTAGGCCATTAAT
1 TTTCATCTAACTTGCATAATTGACAC-TTTCTGTCAAATGCACAACTAGGCCATTAAT
57843 CCTTTATTTT
Statistics
Matches: 672, Mismatches: 80, Indels: 48
0.84 0.10 0.06
Matches are distributed among these distances:
72 1 0.00
73 39 0.06
74 1 0.00
75 2 0.00
76 20 0.03
77 2 0.00
78 20 0.03
79 3 0.00
80 215 0.32
81 364 0.54
82 5 0.01
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (80 bp):
TTTCATCTAACTTGCATAATTGACACTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTACT
CAAAGGTATTTAACC
Found at i:57315 original size:161 final size:161
Alignment explanation
Indices: 56986--57842 Score: 1130
Period size: 161 Copynumber: 5.4 Consensus size: 161
56976 GCATATAGCT
* * * *
56986 TTTCATCTAACTT-GCATGATTGACAACTTCCTGTCAAATGCACAGCTAGGCCATTAATATTTGA
1 TTTCATCTAA-TTGGCATAATTGAC-ACTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTA
** * *
57050 CTCAAAGGTATTTAACCTTTCATCTAACTAACATAATTGATACA-TTCTGTCAAATGCATAACTA
64 CTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTA
* *
57114 GGCCATTAATCTTTTACTCAAAGGTATTTAACG
129 GGCCATTAATATTTTACTCAAAGGTATTTAACC
** * * *
57147 TTTCATCTAACTT-GCATAATTGACATCTTTCTGTCAGTTGCATAGGC-AAGCCATTAATATTTT
1 TTTCATCTAA-TTGGCATAATTGACA-CTTTCTGTCAAATGCACA-ACTAGGCCATTAATATTTT
* *
57210 ACTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGACACATTTCTGTCAAATGCACAGCT
63 ACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACT
**
57275 AGGCCATTAATATTTTACTCAAATATATTTAACC
128 AGGCCATTAATATTTTACTCAAAGGTATTTAACC
* *
57309 -TTCATCTAATTGGCATAATTGACACCTTTATGTCAAATGCACATCTAGGCCATTAATATTTTAC
1 TTTCATCTAATTGGCATAATTGACA-CTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
* * *
57373 TCAAAGGTATTTAACCTTTCATATAACTGGCAT-A-T-ACACCTTTCTATCAAATGCACAA-T--
65 TCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAG
* * * *
57432 --TATTAATCTTTTAGTGAAAGGTATTTAACC
130 GCCATTAATATTTTACTCAAAGGTATTTAACC
* *
57462 TTTCATCTAATTGGCATAATTAACACTTTTCTGTCAAATGCACAACTAGGCCAGTAATATTTTAC
1 TTTCATCTAATTGGCATAATTGACAC-TTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
* * * * *
57527 TCAAAGGTATTTAACCTTTCATCTAACTAGAATAATTGACACAGTTCTGTCAATTGCACAGCTAG
65 TCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAG
* * *
57592 ACCATTAAT-CTTTACTCAAAGGCATTTAACC
130 GCCATTAATATTTTACTCAAAGGTATTTAACC
* *
57623 TTTCATCTAATTGGCATAATTGACACATTTCTATCAAATGCACAACTAGGCCATTAATCTTTTAC
1 TTTCATCTAATTGGCATAATTGACAC-TTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
* * *
57688 TCAAAGATATTGAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAG
65 TCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAG
57753 GCCATTAATATTTTACTCAAAGGTATTTAACC
130 GCCATTAATATTTTACTCAAAGGTATTTAACC
* *
57785 TTTCATCTAACTGGCATAATTGACACATTTCTTTCAAATGCACAACTAGGCCATTAAT
1 TTTCATCTAATTGGCATAATTGACAC-TTTCTGTCAAATGCACAACTAGGCCATTAAT
57843 CCTTTATTTT
Statistics
Matches: 610, Mismatches: 70, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
153 25 0.04
154 88 0.14
155 1 0.00
156 1 0.00
157 19 0.03
158 21 0.03
159 1 0.00
160 5 0.01
161 318 0.52
162 131 0.21
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (161 bp):
TTTCATCTAATTGGCATAATTGACACTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTACT
CAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGG
CCATTAATATTTTACTCAAAGGTATTTAACC
Found at i:57754 original size:242 final size:241
Alignment explanation
Indices: 56986--57848 Score: 1131
Period size: 242 Copynumber: 3.6 Consensus size: 241
56976 GCATATAGCT
* * * * * *
56986 TTTCATCTAACTTGCATGATTGACAACTTCCTGTCAAATGCACAGCTAGGCCATTAATATTTGAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
* *
57051 TCAAAGGTATTTAACCTTTCATCTAACTA-ACATAATTGATACA-TTCTGTCAAATGCATAACTA
66 TCAAAGGTATTTAACCTTTCATCTAACTAGA-ATAATTGACACATTTCTGTCAAATGCACAACTA
*
57114 GGCCATTAAT-CTTTTACTCAAAGGTATTTAACGTTTCATCTAACTT-GCATAATTGACATCTTT
130 GGCCATTAATAC-TTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGGCATAATTGACA-CTTT
* ** * * * *
57177 CTGTCAGTTGCATAGGCAAGCCATTAATATTTTACTCAAAGGTATTTAACC
192 CTATCAAATGCACA-ACTAGCCATTAATCTTTTACTCAAAGGTATTTAACC
* * *
57228 TTTCATCTAACTGGTATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATATTTTAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
** * * * * * *
57293 TCAAATATATTTAACC-TTCATCTAATTGGCATAATTGACACCTTTATGTCAAATGCACATCTAG
66 TCAAAGGTATTTAACCTTTCATCTAACTAGAATAATTGACACATTTCTGTCAAATGCACAACTAG
* * *
57357 GCCATTAATATTTTACTCAAAGGTATTTAACCTTTCATATAACTGGCAT-A-T-ACACCTTTCTA
131 GCCATTAATACTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACA-CTTTCTA
* * *
57419 TCAAATGCACAA-T---TATTAATCTTTTAGTGAAAGGTATTTAACC
195 TCAAATGCACAACTAGCCATTAATCTTTTACTCAAAGGTATTTAACC
* * * *
57462 TTTCATCTAATTGGCATAATTAACACTTTTCTGTCAAATGCACAACTAGGCCAGTAATATTTTAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
* * *
57527 TCAAAGGTATTTAACCTTTCATCTAACTAGAATAATTGACACAGTTCTGTCAATTGCACAGCTAG
66 TCAAAGGTATTTAACCTTTCATCTAACTAGAATAATTGACACATTTCTGTCAAATGCACAACTAG
* *
57592 ACCATTAAT-CTTTACTCAAAGGCATTTAACCTTTCATCTAATTGGCATAATTGACACATTTCTA
131 GCCATTAATACTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACAC-TTTCTA
* *
57656 TCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGATATTGAACC
195 TCAAATGCACAACTA-GCCATTAATCTTTTACTCAAAGGTATTTAACC
57704 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
* * *
57769 TCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTTTCAAATGCACAACTAG
66 TCAAAGGTATTTAACCTTTCATCTAACTAGAATAATTGACACATTTCTGTCAAATGCACAACTAG
*
57834 GCCATTAATCCTTTA
131 GCCATTAATACTTTA
57849 TTTTGGAATA
Statistics
Matches: 537, Mismatches: 69, Indels: 29
0.85 0.11 0.05
Matches are distributed among these distances:
234 134 0.25
235 49 0.09
236 2 0.00
237 21 0.04
238 1 0.00
239 17 0.03
240 1 0.00
241 22 0.04
242 285 0.53
243 5 0.01
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (241 bp):
TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTAATATTTTAC
TCAAAGGTATTTAACCTTTCATCTAACTAGAATAATTGACACATTTCTGTCAAATGCACAACTAG
GCCATTAATACTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACTTTCTAT
CAAATGCACAACTAGCCATTAATCTTTTACTCAAAGGTATTTAACC
Found at i:58076 original size:15 final size:15
Alignment explanation
Indices: 58053--58083 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58043 TTAAGTGTCC
58053 AACAAAAATTCATAA
1 AACAAAAATTCATAA
*
58068 AACAGAAATTCATAA
1 AACAAAAATTCATAA
58083 A
1 A
58084 CTTATTATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.13, G:0.03, T:0.19
Consensus pattern (15 bp):
AACAAAAATTCATAA
Found at i:60029 original size:21 final size:21
Alignment explanation
Indices: 60003--60098 Score: 120
Period size: 21 Copynumber: 4.6 Consensus size: 21
59993 GTTTCCAGAT
* *
60003 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
60024 TCGCAATGCGAACATGGACTA
1 TCGCAATGCGAACTTGGACTA
*
60045 TCGCAATGTGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* **
60066 TCACAATAAGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
60087 TTGCAATGCGAA
1 TCGCAATGCGAA
60099 TATGTAAATC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:60139 original size:21 final size:21
Alignment explanation
Indices: 60113--60329 Score: 126
Period size: 21 Copynumber: 10.3 Consensus size: 21
60103 TAAATCGTAA
60113 TGCGATAGTCGAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCAT
*
60134 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCAT
*
60155 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCAT
** * *
60176 TGCGATTTTCCAAATTCGACTAT
1 TGCGATAGTCGAAGTTCG-C-AT
* *
60199 CGC-A-ACG-CGAACTTCGACTAT
1 TGCGATA-GTCGAAGTTCG-C-AT
* * *
60220 CGC-ATTG-CG-ATTTACATTGCAT
1 TGCGATAGTCGAAGTT-C---GCAT
*
60242 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCAT
*
60263 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCAT
** * *
60284 TGCGATTTTCCAAATTCG--T
1 TGCGATAGTCGAAGTTCGCAT
**
60303 TGCGATAGTCGAAGTTCGTGT
1 TGCGATAGTCGAAGTTCGCAT
60324 TGCGAT
1 TGCGAT
60330 TTATTCCAAA
Statistics
Matches: 154, Mismatches: 29, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
19 15 0.10
20 3 0.02
21 117 0.76
22 6 0.04
23 7 0.05
24 3 0.02
25 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCAT
Found at i:60313 original size:40 final size:42
Alignment explanation
Indices: 60262--60392 Score: 205
Period size: 42 Copynumber: 3.2 Consensus size: 42
60252 CAAGTTCGCA
60262 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
60302 TTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
60344 TTGCGATTGTCGAAGTTTGCGTTCCGATTTATTCC-AATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
60385 TTGCGATA
1 TTGCGATA
60393 TTCCAAAATC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
40 26 0.31
41 15 0.18
42 42 0.51
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:60346 original size:21 final size:20
Alignment explanation
Indices: 60281--60399 Score: 86
Period size: 21 Copynumber: 5.9 Consensus size: 20
60271 TCGAAGTTCG
60281 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* * *
60300 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
60319 CGTGTTGCGATTTATTCCAAATT
1 C--GTTGCGA-TTATTCCAAATT
* * *
60342 CGTTGCGATT-GTCGAAGTTT
1 CGTTGCGATTATTCCAA-ATT
*
60362 GCGTTCCGATTTATTCC-AATT
1 -CGTTGCGA-TTATTCCAAATT
60383 CGTTGCGA-TATTCCAAA
1 CGTTGCGATTATTCCAAA
60400 ATCGCAACGA
Statistics
Matches: 76, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
18 7 0.09
19 21 0.28
20 11 0.14
21 23 0.30
22 3 0.04
23 11 0.14
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:60509 original size:18 final size:16
Alignment explanation
Indices: 60486--60522 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
60476 GACACGTATT
60486 ACCATGACCACGACCACG
1 ACCATGACC-CGACC-CG
60504 ACCATGACCCGACCCG
1 ACCATGACCCGACCCG
60520 ACC
1 ACC
60523 GAGACGAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (16 bp):
ACCATGACCCGACCCG
Found at i:61182 original size:42 final size:42
Alignment explanation
Indices: 61119--61317 Score: 223
Period size: 42 Copynumber: 4.8 Consensus size: 42
61109 TGCGATTTTG
* * *
61119 GACTATAGCAAACGAATTTGGAATAAATCACAATGCGAACTTC
1 GACTATCGC-AACGAATTTGGAATAAATCGCAACGCGAACTTC
* * * *
61162 GACTATCGCAACGAACTTGGACT--ATCGC-A--CGAATTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
61199 GAATAAATCGCAACGAATTTGGAA-AAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
61242 G-CTATCGCAACGAACTTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAA-TTTGGAATAAATCGCAACGCGAACTTC
*
61284 GACTATCGCAACTAATTTGGAATAAATCGCAACG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACG
61318 AATTTGGAAA
Statistics
Matches: 132, Mismatches: 14, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
37 9 0.07
39 17 0.13
40 20 0.15
41 8 0.06
42 51 0.39
43 27 0.20
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:61373 original size:102 final size:103
Alignment explanation
Indices: 61166--61498 Score: 463
Period size: 102 Copynumber: 3.3 Consensus size: 103
61156 AACTTCGACT
61166 ATCGCAA--CGAACTTGGACTATCGC-ACGAATTTGGAATAAATCGCAACGAATTTGGAAAAATC
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAATTTGG-AAAATC
61228 GCAACGCGAACTTCG-CTATCGCAACGAACTTTGGAATAA
65 GCAACGCGAACTTCGACTATCGCAACGAAC-TTGGAATAA
*
61267 ATCGCAACGCGAACTTGGACTATCGCAACTAATTTGGAATAAATCGCAACGAATTTGG-AAATCG
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAAAATCG
61331 CAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
66 CAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
*
61369 ATCGCAACGCGAACTTGGACTATCGCAACGAA-TTGGAATAAATCGCAACAAATTTGGAATACAT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAA-A-AT
* * * * *
61433 CGCAA--CGAA-TTGGAATAAATCGCAACGCGACTTCGACT--
64 CGCAACGCGAACTTCGACT--ATCGCAACG-AACTTGGAATAA
61471 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTGGACTATCGCAA
61499 TAACGAATAT
Statistics
Matches: 214, Mismatches: 8, Indels: 19
0.89 0.03 0.08
Matches are distributed among these distances:
101 36 0.17
102 93 0.43
103 41 0.19
104 44 0.21
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (103 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAAAATCG
CAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:61384 original size:42 final size:41
Alignment explanation
Indices: 61309--61479 Score: 219
Period size: 41 Copynumber: 4.2 Consensus size: 41
61299 TTTGGAATAA
61309 ATCGCAACGAATTTGG---AAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAA-TTGGAATAAATCGCAACGCGAACTTCGACT
*
61348 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAA-TTGGAATAAATCGCAACGCGAACTTCGACT
* * * *
61390 ATCGCAACGAATTGGAATAAATCGCAA--CAAATTTGGAAT
1 ATCGCAACGAATTGGAATAAATCGCAACGCGAACTTCGACT
61429 ACATCGCAACGAATTGGAATAAATCGCAACGCG-ACTTCGACT
1 --ATCGCAACGAATTGGAATAAATCGCAACGCGAACTTCGACT
61471 ATCGCAACG
1 ATCGCAACG
61480 CGAACTTGGA
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
39 24 0.21
40 9 0.08
41 43 0.37
42 39 0.34
43 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAATTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:61426 original size:62 final size:61
Alignment explanation
Indices: 61265--61478 Score: 192
Period size: 60 Copynumber: 3.5 Consensus size: 61
61255 ACTTTGGAAT
* * * *
61265 AAATCGCAACGCGAACTTGGACTATCGCAACTAATTTGGAATAAATCGCAA--CGAATTTGG
1 AAATCGCAAC-CGAACTTCGAATATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGG
* * *
61325 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
1 AAATCGCAAC-CGAACTTCGAATATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGG
* * *
61387 ACTATCGCAA-CGAA-TTGGAATAAATCGCAACAAATTTGGAATACATCGCAA--CGAA-TTGG
1 A-AATCGCAACCGAACTTCGAAT--ATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGG
*
61446 AATAAATCGCAACGCG-ACTTCGACTATCGCAAC
1 ---AAATCGCAAC-CGAACTTCGAATATCGCAAC
61479 GCGAACTTGG
Statistics
Matches: 130, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
59 4 0.03
60 57 0.44
61 19 0.15
62 36 0.28
63 14 0.11
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (61 bp):
AAATCGCAACCGAACTTCGAATATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGG
Found at i:61491 original size:21 final size:19
Alignment explanation
Indices: 61154--61498 Score: 223
Period size: 21 Copynumber: 17.0 Consensus size: 19
61144 AATCACAATG
* *
61154 CGAACTTCGACTATCGCAA
1 CGAACTTGGAATATCGCAA
*
61173 CGAACTTGGACTATCGC-A
1 CGAACTTGGAATATCGCAA
*
61191 CGAATTTGGAATAAATCGCAA
1 CGAACTTGGAAT--ATCGCAA
* *
61212 CGAATTTGGAAAAATCGCAA
1 CGAACTTGG-AATATCGCAA
* *
61232 CGCGAACTTCG-CTATCGCAA
1 --CGAACTTGGAATATCGCAA
61252 CGAACTTTGGAATAAATCGCAA
1 CGAAC-TTGGAAT--ATCGCAA
*
61274 CGCGAACTTGGACTATCGCAA
1 --CGAACTTGGAATATCGCAA
* *
61295 CTAATTTGGAATAAATCGCAA
1 CGAACTTGGAAT--ATCGCAA
*
61316 CGAATTTGGAA-ATCGCAA
1 CGAACTTGGAATATCGCAA
* *
61334 CGCGAACTTCGACTATCGCAA
1 --CGAACTTGGAATATCGCAA
61355 CGAACTTGGAATAAATCGCAA
1 CGAACTTGGAAT--ATCGCAA
*
61376 CGCGAACTTGGACTATCGCAA
1 --CGAACTTGGAATATCGCAA
61397 CGAA-TTGGAATAAATCGCAA
1 CGAACTTGGAAT--ATCGCAA
* *
61417 CAAATTTGGAATACATCGCAA
1 CGAACTTGGAAT--ATCGCAA
61438 CGAA-TTGGAATAAATCGCAA
1 CGAACTTGGAAT--ATCGCAA
* * *
61458 CGCGACTTCGACTATCGCAA
1 CG-AACTTGGAATATCGCAA
*
61478 CGCGAACTTGGACTATCGCAA
1 --CGAACTTGGAATATCGCAA
61499 TAACGAATAT
Statistics
Matches: 267, Mismatches: 31, Indels: 54
0.76 0.09 0.15
Matches are distributed among these distances:
18 29 0.11
19 42 0.16
20 62 0.23
21 89 0.33
22 23 0.09
23 17 0.06
24 5 0.02
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (19 bp):
CGAACTTGGAATATCGCAA
Done.