Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022512.1 Corchorus olitorius cultivar O-4 contig22545, 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: 64879
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8186 original size:107 final size:105
Alignment explanation
Indices: 7937--8197 Score: 352
Period size: 107 Copynumber: 2.5 Consensus size: 105
7927 TTTAATTTTC
* ** *
7937 TAACCCTTAAAATAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAGTTATATATTT
1 TAACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTT
* * * *
8000 TATTTCTAGAACCCTATAACAATATTATTAATTATGGAAT
66 TATTTCCAAAACCCTATAACAAAATTATTAATTATGAAAT
* * *
8040 TTACCCTT--AA-AAAAATAAAATTTTAATTTGGGGCTAAACTTATTGAAATTAGTTTTATATTT
1 TAACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTT
*
8102 TATTTCCAAAACCCTATAACAAAAAATTATTAATTTTGAAAT
66 TATTTCCAAAACCCTATAAC--AAAATTATTAATTATGAAAT
*
8144 TAACCCTTAAAATAAAAATAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTA
1 TAACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
8198 AGGCTAAACT
Statistics
Matches: 136, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
100 16 0.12
101 15 0.11
102 33 0.24
103 7 0.05
104 24 0.18
106 2 0.01
107 39 0.29
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (105 bp):
TAACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTT
TATTTCCAAAACCCTATAACAAAATTATTAATTATGAAAT
Found at i:17215 original size:20 final size:20
Alignment explanation
Indices: 17198--17240 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17188 AAAAAAATTA
*
17198 ATAGATAAATAAATAAATAG
1 ATAGAAAAATAAATAAATAG
*
17218 ATAGAAAAATAAATAAAAAG
1 ATAGAAAAATAAATAAATAG
17238 ATA
1 ATA
17241 AATAGGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (20 bp):
ATAGAAAAATAAATAAATAG
Found at i:17227 original size:16 final size:15
Alignment explanation
Indices: 17189--17232 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
17179 ATATTAAAAA
*
17189 AAAAAATTAATAGAT
1 AAAAAATAAATAGAT
17204 AAATAAATAAATAGAT
1 AAA-AAATAAATAGAT
17220 AGAAAAATAAATA
1 A-AAAAATAAATA
17233 AAAAGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 21 0.81
17 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (15 bp):
AAAAAATAAATAGAT
Found at i:17241 original size:12 final size:11
Alignment explanation
Indices: 17202--17244 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
17192 AAATTAATAG
17202 ATAAATAAATAA
1 ATAAATAAA-AA
*
17214 ATAGATAGAAAA
1 ATAAATA-AAAA
17226 ATAAATAAAAA
1 ATAAATAAAAA
17237 GATAAATA
1 -ATAAATA
17245 GGTATATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 21 0.78
13 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (11 bp):
ATAAATAAAAA
Found at i:17257 original size:24 final size:24
Alignment explanation
Indices: 17230--17292 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
17220 AGAAAAATAA
* *
17230 ATAAAAAGATAAATAGGTATATAG
1 ATAAATAGATAAATAGGTATAGAG
* *
17254 ATAATTAGATAAAGAGGTATAGAG
1 ATAAATAGATAAATAGGTATAGAG
17278 ATAAATAGATAAATA
1 ATAAATAGATAAATA
17293 TGTAGGTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.25
Consensus pattern (24 bp):
ATAAATAGATAAATAGGTATAGAG
Found at i:17287 original size:8 final size:8
Alignment explanation
Indices: 17197--17292 Score: 67
Period size: 8 Copynumber: 12.5 Consensus size: 8
17187 AAAAAAAATT
17197 AATAGATA
1 AATAGATA
*
17205 AATAAATA
1 AATAGATA
17213 AATAGATA
1 AATAGATA
*
17221 GAA-AAATA
1 -AATAGATA
17229 AAT--A-A
1 AATAGATA
17234 AA-AGATA
1 AATAGATA
*
17241 AATAGGTA
1 AATAGATA
*
17249 TATAGATA
1 AATAGATA
*
17257 ATTAGATA
1 AATAGATA
* *
17265 AAGAGGTA
1 AATAGATA
* *
17273 TAGAGATA
1 AATAGATA
17281 AATAGATA
1 AATAGATA
17289 AATA
1 AATA
17293 TGTAGGTAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
5 3 0.04
6 2 0.03
7 5 0.07
8 55 0.82
9 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (8 bp):
AATAGATA
Found at i:17325 original size:4 final size:4
Alignment explanation
Indices: 17316--17421 Score: 53
Period size: 4 Copynumber: 26.5 Consensus size: 4
17306 AGATAATAGC
** * *
17316 AATA AATA AATA GATATA GCTA AATT AATA AATA AA-A AGATA AAT- AGTA
1 AATA AATA AATA -A-ATA AATA AATA AATA AATA AATA A-ATA AATA AATA
* * *
17365 AATA AATA GATA AGAGTT AA-A AATA AATA AA-A AGATA AAT- AGTA AATA
1 AATA AATA AATA A-A-TA AATA AATA AATA AATA A-ATA AATA AATA AATA
17413 AAT- AATA AA
1 AATA AATA AA
17422 AATCTTTTTG
Statistics
Matches: 76, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
3 13 0.17
4 51 0.67
5 7 0.09
6 5 0.07
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:17368 original size:19 final size:19
Alignment explanation
Indices: 17344--17414 Score: 70
Period size: 19 Copynumber: 3.4 Consensus size: 19
17334 GCTAAATTAA
17344 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
17363 TAAATAAATAGATAAGAGTTAAAAA
1 TAAATAAAAAGATAA-A--T---AG
17388 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
17407 TAAATAAA
1 TAAATAAA
17415 TAATAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 23 0.55
20 1 0.02
22 2 0.05
24 1 0.02
25 15 0.36
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (19 bp):
TAAATAAAAAGATAAATAG
Found at i:17401 original size:44 final size:45
Alignment explanation
Indices: 17318--17420 Score: 158
Period size: 44 Copynumber: 2.3 Consensus size: 45
17308 ATAATAGCAA
*
17318 TAAATAAATAGAT-ATAGCTAAATTAATAAATAAAAAGATAAATAG
1 TAAATAAATAGATAAGAGCTAAA-TAATAAATAAAAAGATAAATAG
*
17363 TAAATAAATAGATAAGAGTTAAA-AATAAATAAAAAGATAAATAG
1 TAAATAAATAGATAAGAGCTAAATAATAAATAAAAAGATAAATAG
17407 TAAATAAATA-ATAA
1 TAAATAAATAGATAA
17421 AAATCTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
43 4 0.07
44 31 0.56
45 13 0.24
46 7 0.13
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.25
Consensus pattern (45 bp):
TAAATAAATAGATAAGAGCTAAATAATAAATAAAAAGATAAATAG
Found at i:18905 original size:54 final size:54
Alignment explanation
Indices: 18844--18963 Score: 204
Period size: 54 Copynumber: 2.2 Consensus size: 54
18834 ACGGAAACCT
* * *
18844 TTCTTGGAATGACTGCACTGGACCTTTTGGGGATCAACTCTGACCATTGAAAAC
1 TTCTTGGAATGACCGCACTGAACCTTTTAGGGATCAACTCTGACCATTGAAAAC
*
18898 TTCTTGGAATGACCGCACTGAATCTTTTAGGGATCAACTCTGACCATTGAAAAC
1 TTCTTGGAATGACCGCACTGAACCTTTTAGGGATCAACTCTGACCATTGAAAAC
18952 TTCTTGGAATGA
1 TTCTTGGAATGA
18964 GATCAACTCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (54 bp):
TTCTTGGAATGACCGCACTGAACCTTTTAGGGATCAACTCTGACCATTGAAAAC
Found at i:18968 original size:35 final size:35
Alignment explanation
Indices: 18929--19518 Score: 849
Period size: 35 Copynumber: 16.6 Consensus size: 35
18919 ATCTTTTAGG
* ** *
18929 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
18964 GATCAACTCTGATCATAAAAAAAACTTCTTAAAATGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAATGA
*
19001 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* * **
19036 GATCAACTCTGATAATCAAAAACTTCTTGAAACAA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
19071 GATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
19106 GATCAACTCTGATTATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
** *
19141 GATCAACTCTGATCATCGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
19176 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
19211 GATCAACTCTGATCA-ACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATA-AAAAACTTCTTGAAATGA
*
19246 GATCAACTCTGATCATAAAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
19281 GATCAACTCTGATCATAAAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAATGA
*
19318 GATCAACTCTGATCATAAAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
19353 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT---AAAAAACTTCTTGAAATGA
*
19391 GATCAACTCTGATCATAAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAATGA
* *
19427 GATCAATTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
19462 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
19497 GATCAACTCTGATCATAAAAAA
1 GATCAACTCTGATCATAAAAAA
19519 AACTTCATGG
Statistics
Matches: 506, Mismatches: 40, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
35 374 0.74
36 35 0.07
37 64 0.13
38 33 0.07
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
Found at i:19587 original size:54 final size:53
Alignment explanation
Indices: 19517--19902 Score: 389
Period size: 54 Copynumber: 7.2 Consensus size: 53
19507 GATCATAAAA
* * *
19517 AAAACTTCATGGAATGACCGCACCGGTTCATCTGGGGATCAACTCTGATCTCT
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCTCT
* *
19570 AAGAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCCGATCACT
1 AA-AACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCTCT
** ** *
19624 GAAAACTTCTTTTAAATGATTGCACTGGATCATCTAGGGATCAACTCTGATCTCT
1 -AAAACTTC-TTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCTCT
* * * ** * ***
19679 AAAACTTATAGGAATAACCGCACTGGGCCATCT-GGAATCAACTCTGATCAAAG
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATC-TCT
* *
19732 AAAACTTCTTGGAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCACT
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCTCT
* * ** * *
19785 GAAAACTTCTTGAAATGATCGCACTAAATCATTTGGGGATCAACTCTAATCAT-T
1 -AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATC-TCT
* * * * * *
19839 CAAAACTTTTTAGAATGATCTCACTGGACCATCTGCGGATCAACTCTGATCTCT
1 -AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCTCT
19893 AAAATCTTCT
1 AAAA-CTTCT
19903 ATGAAAGATA
Statistics
Matches: 270, Mismatches: 54, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
52 15 0.06
53 53 0.20
54 162 0.60
55 40 0.15
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (53 bp):
AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCTCT
Found at i:19740 original size:161 final size:159
Alignment explanation
Indices: 19517--19889 Score: 457
Period size: 161 Copynumber: 2.3 Consensus size: 159
19507 GATCATAAAA
* ** *
19517 AAAACTTCAT-GGAATGACCGCACCGGTTCATCTGGGGATCAACTCTGATCTCTAAGAACTTCTT
1 AAAACTT-ATAGGAATGACCGCACTGGACCATCT-GGGATCAACTCTGA--TCAAAGAACTTCTT
* * *
19581 GGAATGACCGCACTGGATCATCTGGGGATCAACTCCGATCACTGAAAACTTCTTTTAAATGATTG
62 GGAATGACCGCACTGGATCATCTGAGGATCAACTCCGATCACTGAAAACTTC-TTGAAATGATCG
** *
19646 CACTGGATCATCTAGGGATCAACTCTGATC--TC
126 CACTAAATCATCTAGGGATCAACTCTAATCATTC
* * *
19678 TAAAACTTATAGGAATAACCGCACTGGGCCATCTGGAATCAACTCTGATCAAAGAAAACTTCTTG
1 -AAAACTTATAGGAATGACCGCACTGGACCATCTGGGATCAACTCTGATCAAAG--AACTTCTTG
*
19743 GAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCACTGAAAACTTCTTGAAATGATCGCA
63 GAATGACCGCACTGGATCATCTGAGGATCAACTCCGATCACTGAAAACTTCTTGAAATGATCGCA
* *
19808 CTAAATCATTTGGGGATCAACTCTAATCATTC
128 CTAAATCATCTAGGGATCAACTCTAATCATTC
* * *
19840 AAAACTTTTTA-GAATGATCTCACTGGACCATCTGCGGATCAACTCTGATC
1 AAAAC-TTATAGGAATGACCGCACTGGACCATCTG-GGATCAACTCTGATC
19890 TCTAAAATCT
Statistics
Matches: 183, Mismatches: 21, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
159 5 0.03
160 35 0.19
161 97 0.53
162 46 0.25
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (159 bp):
AAAACTTATAGGAATGACCGCACTGGACCATCTGGGATCAACTCTGATCAAAGAACTTCTTGGAA
TGACCGCACTGGATCATCTGAGGATCAACTCCGATCACTGAAAACTTCTTGAAATGATCGCACTA
AATCATCTAGGGATCAACTCTAATCATTC
Found at i:19781 original size:215 final size:215
Alignment explanation
Indices: 19498--19896 Score: 565
Period size: 215 Copynumber: 1.9 Consensus size: 215
19488 TTGAAATGAG
* *
19498 ATCAACTCTGATCATAAAAAAAACTTCATGGAATGACCGCACCGGTTCATCTGGGGATCAACTCT
1 ATCAACTCTGATCA-AAAAAAAACTTCATGGAATGACCGCACCGGATCATCTGAGGATCAACTCT
* * ** * *
19563 GATCTCT-AAGAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCCGATCACTGAA
65 GATCACTGAA-AACTTCTTGAAATGACCGCACTAAATCATCTGGGGATCAACTCCAATCACTCAA
*
19627 AACTTCTTTTA-AATGAT-TGCACTGGATCATCTAG-GGATCAACTCTGATCTCTAAAACTTATA
129 AAC-T-TTTTAGAATGATCT-CACTGGACCATCT-GCGGATCAACTCTGATCTCTAAAACTTATA
19689 GGAATAACCGCACTGGGCCATCTGGA
190 GGAATAACCGCACTGGGCCATCTGGA
* * *
19715 ATCAACTCTGATC-AAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTGAGGATCAACTCTG
1 ATCAACTCTGATCAAAAAAAAACTTCATGGAATGACCGCACCGGATCATCTGAGGATCAACTCTG
* * * *
19779 ATCACTGAAAACTTCTTGAAATGATCGCACTAAATCATTTGGGGATCAACTCTAATCATTCAAAA
66 ATCACTGAAAACTTCTTGAAATGACCGCACTAAATCATCTGGGGATCAACTCCAATCACTCAAAA
19844 CTTTTTAGAATGATCTCACTGGACCATCTGCGGATCAACTCTGATCTCTAAAA
131 CTTTTTAGAATGATCTCACTGGACCATCTGCGGATCAACTCTGATCTCTAAAA
19897 TCTTCTATGA
Statistics
Matches: 162, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
213 6 0.04
214 41 0.25
215 100 0.62
216 2 0.01
217 13 0.08
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (215 bp):
ATCAACTCTGATCAAAAAAAAACTTCATGGAATGACCGCACCGGATCATCTGAGGATCAACTCTG
ATCACTGAAAACTTCTTGAAATGACCGCACTAAATCATCTGGGGATCAACTCCAATCACTCAAAA
CTTTTTAGAATGATCTCACTGGACCATCTGCGGATCAACTCTGATCTCTAAAACTTATAGGAATA
ACCGCACTGGGCCATCTGGA
Found at i:19976 original size:52 final size:53
Alignment explanation
Indices: 19920--20026 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 53
19910 ATAACACCGA
* * *
19920 GTCATCTGAAGATCAACTT-ATCTTTGA-AAGCTTCTATGAAAGACCGCAAAGG
1 GTCATCTGAAAATCAACTTAATCTCTGAGAA-CTTCAATGAAAGACCGCAAAGG
* * *
19972 GTCATTTTAAAATCAACTTAGATCTCTGAGAACTTCAATGAAAGACCGCACAGG
1 GTCATCTGAAAATCAACTTA-ATCTCTGAGAACTTCAATGAAAGACCGCAAAGG
20026 G
1 G
20027 CTTAGATCTC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
52 16 0.35
54 28 0.61
55 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (53 bp):
GTCATCTGAAAATCAACTTAATCTCTGAGAACTTCAATGAAAGACCGCAAAGG
Found at i:20052 original size:39 final size:39
Alignment explanation
Indices: 19988--20065 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
19978 TTAAAATCAA
*
19988 CTTAGATCTCTGAGAACTTCAATGAAAGACCGCACAGGG
1 CTTAGATCTCTGAGAACTTCAATGAAAGACCGCAAAGGG
*
20027 CTTAGATCTCTGA-AAGCTTCTATGAAAGACCGCAAAGGG
1 CTTAGATCTCTGAGAA-CTTCAATGAAAGACCGCAAAGGG
20066 TCTTTTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 2 0.06
39 34 0.94
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (39 bp):
CTTAGATCTCTGAGAACTTCAATGAAAGACCGCAAAGGG
Found at i:20105 original size:92 final size:93
Alignment explanation
Indices: 19939--20118 Score: 308
Period size: 92 Copynumber: 1.9 Consensus size: 93
19929 AGATCAACTT
* * *
19939 ATCTTTGAAAGCTTCTATGAAAGACCGCAAAGGGTCATTTTAAAATCAACTTAGATCTCTGAGAA
1 ATCTCTGAAAGCTTCTATGAAAGACCGCAAAGGGTCATTTTAAAATCAACTTAAATCTCTGAAAA
20004 CTTCAATGAAAGACCGCACAGGGCTTAG
66 CTTCAATGAAAGACCGCACAGGGCTTAG
*
20032 ATCTCTGAAAGCTTCTATGAAAGACCGCAAAGGGTC-TTTTAAGATCAACTTAAATCTCTGAAAA
1 ATCTCTGAAAGCTTCTATGAAAGACCGCAAAGGGTCATTTTAAAATCAACTTAAATCTCTGAAAA
*
20096 CTTCTATGAAAGACCGCACAGGG
66 CTTCAATGAAAGACCGCACAGGG
20119 TGCTTGAAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 47 0.57
93 35 0.43
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (93 bp):
ATCTCTGAAAGCTTCTATGAAAGACCGCAAAGGGTCATTTTAAAATCAACTTAAATCTCTGAAAA
CTTCAATGAAAGACCGCACAGGGCTTAG
Found at i:21296 original size:37 final size:40
Alignment explanation
Indices: 21222--21300 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 40
21212 TTTTGAGAAA
* **
21222 AAAACATTTTTTCTCATTTTGAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTCTCATTTTGAAAAAATCACACTTTGAGG
*
21262 AAAACA-TTTTTC-C-TTTTGAAAAAATCACAGTTTGAGG
1 AAAACATTTTTTCTCATTTTGAAAAAATCACACTTTGAGG
21299 AA
1 AA
21301 GGTTTCATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 22 0.63
38 1 0.03
39 6 0.17
40 6 0.17
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (40 bp):
AAAACATTTTTTCTCATTTTGAAAAAATCACACTTTGAGG
Found at i:24541 original size:8 final size:8
Alignment explanation
Indices: 24530--24790 Score: 105
Period size: 8 Copynumber: 33.1 Consensus size: 8
24520 ATAAAAAAAT
24530 AATAGATA
1 AATAGATA
*
24538 AATACATA
1 AATAGATA
24546 AATAGATA
1 AATAGATA
*
24554 GAA-AAATA
1 -AATAGATA
24562 AATA-A-A
1 AATAGATA
24568 AATA-ATA
1 AATAGATA
* *
24575 GATAAATA
1 AATAGATA
*
24583 AAAAGATA
1 AATAGATA
*
24591 AATAGGTA
1 AATAGATA
*
24599 TATAGATA
1 AATAGATA
*
24607 ATTAGATA
1 AATAGATA
* *
24615 AAGAGGTA
1 AATAGATA
* *
24623 TAGAGATA
1 AATAGATA
24631 AATAGATA
1 AATAGATA
*
24639 AATAGGTA
1 AATAGATA
**
24647 GGTA-A-A
1 AATAGATA
*
24653 AAAAGAT-
1 AATAGATA
*
24660 AATAG--C
1 AATAGATA
*
24666 AATAAATA
1 AATAGATA
24674 AATAGATA
1 AATAGATA
* * *
24682 TAGCTAAATT
1 -A-ATAGATA
*
24692 AATAAATA
1 AATAGATA
*
24700 AAAAGATA
1 AATAGATA
24708 AATAG-TA
1 AATAGATA
*
24715 AATAAATA
1 AATAGATA
*
24723 AAAAGATA
1 AATAGATA
24731 AATAGTAACTA
1 AATAG--A-TA
24742 AATAGAT-
1 AATAGATA
*
24749 AATAGTTAAA
1 AATAG--ATA
*
24759 AATAAATA
1 AATAGATA
*
24767 AAAAGATA
1 AATAGATA
24775 AATAG-TA
1 AATAGATA
*
24782 AATAAATA
1 AATAGATA
24790 A
1 A
24791 TAAAAATCTT
Statistics
Matches: 184, Mismatches: 50, Indels: 38
0.68 0.18 0.14
Matches are distributed among these distances:
6 12 0.07
7 29 0.16
8 121 0.66
9 6 0.03
10 9 0.05
11 7 0.04
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.24
Consensus pattern (8 bp):
AATAGATA
Found at i:24564 original size:4 final size:4
Alignment explanation
Indices: 24513--24594 Score: 53
Period size: 4 Copynumber: 20.2 Consensus size: 4
24503 AATTATATTA
* * * *
24513 AAAT AAAAT AAAA AAAT -AAT AGAT AAAT ACAT AAAT AGAT AGAA- AAAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT
* *
24561 AAAT AAAA ATAAT AGAT AAAT AAA- AAGAT AAAT A
1 AAAT AAAT A-AAT AAAT AAAT AAAT AA-AT AAAT A
24595 GGTATATAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 13
0.70 0.14 0.15
Matches are distributed among these distances:
3 7 0.12
4 42 0.71
5 10 0.17
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:24675 original size:4 final size:4
Alignment explanation
Indices: 24666--24794 Score: 58
Period size: 4 Copynumber: 32.5 Consensus size: 4
24656 AGATAATAGC
** * *
24666 AATA AATA AATA GATATA GCTA AATT AATA AATA AA-A AGATA AAT- AGTA
1 AATA AATA AATA -A-ATA AATA AATA AATA AATA AATA A-ATA AATA AATA
* * * *
24715 AATA AATA AA-A AGATA AAT- AGTA ACTA AATA GATA ATAGTT AA-A AATA
1 AATA AATA AATA A-ATA AATA AATA AATA AATA AATA A-A-TA AATA AATA
*
24763 AATA AA-A AGATA AAT- AGTA AATA AAT- AATA AA
1 AATA AATA A-ATA AATA AATA AATA AATA AATA AA
24795 AATCTTTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 30
0.66 0.12 0.21
Matches are distributed among these distances:
3 17 0.18
4 62 0.67
5 9 0.10
6 5 0.05
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:24695 original size:26 final size:26
Alignment explanation
Indices: 24666--24750 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 26
24656 AGATAATAGC
* *
24666 AATAAATAAATAGAT-ATAGCTAAATT
1 AATAAATAAAAAGATAATAG-TAAATA
*
24692 AATAAATAAAAAGATAA-A-T-AGTA
1 AATAAATAAAAAGATAATAGTAAATA
*
24715 AATAAATAAAAAGATAAATAGTAACTA
1 AATAAATAAAAAGAT-AATAGTAAATA
*
24742 AATAGATAA
1 AATAAATAA
24751 TAGTTAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
23 17 0.35
24 3 0.06
25 1 0.02
26 16 0.33
27 12 0.24
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (26 bp):
AATAAATAAAAAGATAATAGTAAATA
Found at i:24778 original size:26 final size:25
Alignment explanation
Indices: 24740--24796 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
24730 AAATAGTAAC
* *
24740 TAAATAGATAATAGTTAA-AAATAAA
1 TAAAAAGATAATAGTAAATAAAT-AA
24765 TAAAAAGATAAATAGTAAATAAATAA
1 TAAAAAGAT-AATAGTAAATAAATAA
24791 TAAAAA
1 TAAAAA
24797 TCTTTTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.29
26 16 0.57
27 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (25 bp):
TAAAAAGATAATAGTAAATAAATAA
Found at i:28734 original size:66 final size:66
Alignment explanation
Indices: 28628--28810 Score: 267
Period size: 66 Copynumber: 2.8 Consensus size: 66
28618 ACGCACATAT
* * *
28628 GGGGATGCCGGAGAAAGACAAAATGCATTTGGCAGTTTTGACAATACCCCAGATTTCAAGGAGTC
1 GGGGATGCCGGAGAAAGACACAATGCATTTGGGAGTTTTGACAAAACCCCAGATTTCAAGGAGTC
28693 A
66 A
* * ** *
28694 GGGGATGCTGGAGAAAGACACAATGCATTTGGGGGTTTTGACAAAACGACAGATTTCAATGAGTC
1 GGGGATGCCGGAGAAAGACACAATGCATTTGGGAGTTTTGACAAAACCCCAGATTTCAAGGAGTC
28759 A
66 A
** *
28760 GATGATGCCGGAGAAAGACACAATACATTTGGGAGTTTTGACAAAACCCCA
1 GGGGATGCCGGAGAAAGACACAATGCATTTGGGAGTTTTGACAAAACCCCA
28811 ACGAAGCAGG
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 102 1.00
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.21
Consensus pattern (66 bp):
GGGGATGCCGGAGAAAGACACAATGCATTTGGGAGTTTTGACAAAACCCCAGATTTCAAGGAGTC
A
Found at i:32820 original size:34 final size:34
Alignment explanation
Indices: 32777--32849 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
32767 ACCAATGCTC
32777 TTTACATTTTGCCTCTGCCACTGTTAATAAGTGA
1 TTTACATTTTGCCTCTGCCACTGTTAATAAGTGA
*
32811 TTTACATTTTGCCTCTGCCACTGTTAATAGGTGA
1 TTTACATTTTGCCTCTGCCACTGTTAATAAGTGA
32845 TTTAC
1 TTTAC
32850 CCAACGCGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.42
Consensus pattern (34 bp):
TTTACATTTTGCCTCTGCCACTGTTAATAAGTGA
Found at i:36431 original size:31 final size:31
Alignment explanation
Indices: 36393--36515 Score: 237
Period size: 31 Copynumber: 4.0 Consensus size: 31
36383 CTACTCACAC
*
36393 TTAACTTCTCCAATTTACCCCTCCATTTTTA
1 TTAACTTCTCCCATTTACCCCTCCATTTTTA
36424 TTAACTTCTCCCATTTACCCCTCCATTTTTA
1 TTAACTTCTCCCATTTACCCCTCCATTTTTA
36455 TTAACTTCTCCCATTTACCCCTCCATTTTTA
1 TTAACTTCTCCCATTTACCCCTCCATTTTTA
36486 TTAACTTCTCCCATTTACCCCTCCATTTTT
1 TTAACTTCTCCCATTTACCCCTCCATTTTT
36516 TTATAAAATT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 91 1.00
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.46
Consensus pattern (31 bp):
TTAACTTCTCCCATTTACCCCTCCATTTTTA
Found at i:47190 original size:24 final size:24
Alignment explanation
Indices: 47158--47212 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
47148 TCAACAAAAG
47158 AACCTTATCTTAGATATATGAATA
1 AACCTTATCTTAGATATATGAATA
47182 AACCTTATCTTAGATATATGAATA
1 AACCTTATCTTAGATATATGAATA
*
47206 AATCTTA
1 AACCTTA
47213 CGTATGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (24 bp):
AACCTTATCTTAGATATATGAATA
Found at i:47279 original size:17 final size:17
Alignment explanation
Indices: 47257--47292 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
47247 GCCGGAATCG
47257 GGGTAGAATCAGTGTAA
1 GGGTAGAATCAGTGTAA
47274 GGGTAGAATCAGTGTAA
1 GGGTAGAATCAGTGTAA
47291 GG
1 GG
47293 TTTTGTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.39, T:0.22
Consensus pattern (17 bp):
GGGTAGAATCAGTGTAA
Found at i:47885 original size:6 final size:6
Alignment explanation
Indices: 47875--47913 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
47865 CATCATCTTC
* *
47875 AGATGA TGATGA TGATGA AGATGA AGATGA AGATGA AGA
1 AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA AGA
47914 AATATTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.21
Consensus pattern (6 bp):
AGATGA
Found at i:48047 original size:6 final size:6
Alignment explanation
Indices: 48034--48069 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
48024 AATCATCATC
* *
48034 TGAAGA TGATGA TGATGA TGAAGA TGAAGA TGAAGA
1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA
48070 GATATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (6 bp):
TGAAGA
Found at i:48123 original size:156 final size:160
Alignment explanation
Indices: 47817--48130 Score: 546
Period size: 156 Copynumber: 2.0 Consensus size: 160
47807 CTTTGATGGG
47817 CGTGTATAGCTTCACTTTGTGCAACTATTGCACTGGTCAAATCAAAATCATCATCTTCAGATGAT
1 CGTGTATAGCTTCACTTTGTGCAACTATTGCACTGGTCAAATCAAAATCATCATCTT-AGA-GAT
*
47882 GATGATGATGAAGATGAAGATGAAGATGAAGAAATATTATAAGCAAAGTTATGATTTGAACTCAT
64 GATGATGATGAAGATGAAGATGAAGATGAAGAAATATTATAAGCAAAGTTATGATGTGAACTCAT
47947 CCTTGCATAAAAGAAAATATTATAAGGTTGGA
129 CCTTGCATAAAAGAAAATATTATAAGGTTGGA
47979 CGTGTATAGCTTCACTTTGTGCAACTATTGCACTGGTCAAATCAAAATCATCATC-T-GA-A-GA
1 CGTGTATAGCTTCACTTTGTGCAACTATTGCACTGGTCAAATCAAAATCATCATCTTAGAGATGA
* *
48040 TGATGATGATGATGAAGATGAAGATGAAGAGATATTATAAGCAAAGTTATGATGTGAACTCATCC
66 TGATGATGAAGATGAAGATGAAGATGAAGAAATATTATAAGCAAAGTTATGATGTGAACTCATCC
*
48105 TTGCATAAAAGAAAATATTTTAAGGT
131 TTGCATAAAAGAAAATATTATAAGGT
48131 CTTTTGGAAT
Statistics
Matches: 148, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
156 89 0.60
157 1 0.01
159 2 0.01
161 1 0.01
162 55 0.37
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (160 bp):
CGTGTATAGCTTCACTTTGTGCAACTATTGCACTGGTCAAATCAAAATCATCATCTTAGAGATGA
TGATGATGAAGATGAAGATGAAGATGAAGAAATATTATAAGCAAAGTTATGATGTGAACTCATCC
TTGCATAAAAGAAAATATTATAAGGTTGGA
Found at i:51956 original size:2 final size:2
Alignment explanation
Indices: 51949--51989 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
51939 ATACTTAAAC
* *
51949 AT AT AT AT AT AT AT AT AT AT TT AT TT A- 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
51990 TTATTAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:51981 original size:17 final size:17
Alignment explanation
Indices: 51949--51992 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
51939 ATACTTAAAC
*
51949 ATATATATAT-ATATAT
1 ATATATATTTAATATAT
*
51965 ATATTTATTTAATATAT
1 ATATATATTTAATATAT
51982 ATATATATTTA
1 ATATATATTTA
51993 TTAAATCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATATTTAATATAT
Found at i:51981 original size:21 final size:21
Alignment explanation
Indices: 51955--51994 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
51945 AAACATATAT
51955 ATATATATATATATTTATTTA
1 ATATATATATATATTTATTTA
51976 ATATATATATATATTTATT
1 ATATATATATATATTTATT
51995 AAATCATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATATATATATTTATTTA
Found at i:56672 original size:2 final size:2
Alignment explanation
Indices: 56665--56702 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
56655 TATTGTTTTC
56665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
56703 ATTCATAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57405 original size:2 final size:2
Alignment explanation
Indices: 57398--57446 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
57388 TAACAAGTAA
*
57398 TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
57440 TG TG TG T
1 TG TG TG T
57447 CTATATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Done.