Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013225.1 Corchorus olitorius cultivar O-4 contig13258, 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: 69700
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4180 original size:29 final size:30
Alignment explanation
Indices: 4139--4196 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
4129 AAAATTTTGA
*
4139 ATTTGAAAATTCATGG-GACAAAATGTCCTG
1 ATTTGAAAATTCATGGAG-CAAAACGTCCTG
*
4169 ATTTG-AAGTTCATGGAGCAAAACGTCCT
1 ATTTGAAAATTCATGGAGCAAAACGTCCT
4197 TGACTCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (30 bp):
ATTTGAAAATTCATGGAGCAAAACGTCCTG
Found at i:23439 original size:13 final size:13
Alignment explanation
Indices: 23421--23445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23411 ATCACAAAAA
23421 AATAATATATAAC
1 AATAATATATAAC
23434 AATAATATATAA
1 AATAATATATAA
23446 AAATTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAATATATAAC
Found at i:24768 original size:6 final size:6
Alignment explanation
Indices: 24757--24781 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
24747 AAAGGGCCTC
24757 TGAAAA TGAAAA TGAAAA TGAAAA T
1 TGAAAA TGAAAA TGAAAA TGAAAA T
24782 AAAGCATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (6 bp):
TGAAAA
Found at i:27067 original size:35 final size:33
Alignment explanation
Indices: 26996--27083 Score: 106
Period size: 35 Copynumber: 2.6 Consensus size: 33
26986 AGGTATTAGT
* *
26996 AAACACCATAGACACTTCTATTGCCAAAAAAAA
1 AAACACAATAGACACTTCAATTGCCAAAAAAAA
27029 AAACACAATAGACACTTCAA-TGTCCAAAAAAAAAA
1 AAACACAATAGACACTTCAATTG-CC--AAAAAAAA
**
27064 AAACACTGTAGACACTTCAA
1 AAACACAATAGACACTTCAA
27084 AGCTCAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 2 0.04
33 20 0.42
35 26 0.54
ACGTcount: A:0.53, C:0.23, G:0.07, T:0.17
Consensus pattern (33 bp):
AAACACAATAGACACTTCAATTGCCAAAAAAAA
Found at i:32494 original size:130 final size:133
Alignment explanation
Indices: 32360--32621 Score: 413
Period size: 131 Copynumber: 2.0 Consensus size: 133
32350 TGTTTAAACT
* *
32360 TTTTATAGTTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTAAATGTAATATCCTTATAACT
1 TTTTATAGTTCTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
* * * * * *
32424 ATTTAATTTTTACCATTTTATTATTTTAATT-AAAATACTTATATATATTAGAATTTT-TAAATA
66 ATTTAATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGACATATTAGAATTTTAAAAATA
32487 TAC
131 TAC
*
32490 TTTTATAGTTCTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATACCT
1 TTTTATAGTTCTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
*
32555 ATTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGACATATTAGAATTTTAAAAATA
66 ATTTAATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGACATATTAGAATTTTAAAAATA
32620 TA
131 TA
32622 TCTTAAATGA
Statistics
Matches: 119, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
130 29 0.24
131 60 0.50
132 23 0.19
133 7 0.06
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (133 bp):
TTTTATAGTTCTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
ATTTAATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGACATATTAGAATTTTAAAAATA
TAC
Found at i:33288 original size:16 final size:16
Alignment explanation
Indices: 33247--33281 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33237 TTTGGCCTCA
*
33247 GGTCACTCGGGTTCTG
1 GGTCATTCGGGTTCTG
*
33263 GGTCATTCGGGTTTTG
1 GGTCATTCGGGTTCTG
33279 GGT
1 GGT
33282 TTTTCGGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.40, T:0.37
Consensus pattern (16 bp):
GGTCATTCGGGTTCTG
Found at i:34180 original size:32 final size:32
Alignment explanation
Indices: 34134--34206 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
34124 ATTTTGTTCC
34134 TGAACTTTATATCAGTTGGAAGCTTTGCCACT
1 TGAACTTTATATCAGTTGGAAGCTTTGCCACT
*
34166 TGAATTTTATATCAGTTGGAAGCTTTGCCACT
1 TGAACTTTATATCAGTTGGAAGCTTTGCCACT
34198 TGAACTTTA
1 TGAACTTTA
34207 ATTTTGAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (32 bp):
TGAACTTTATATCAGTTGGAAGCTTTGCCACT
Found at i:38181 original size:59 final size:59
Alignment explanation
Indices: 38087--38217 Score: 226
Period size: 59 Copynumber: 2.2 Consensus size: 59
38077 GACATTCTTG
*
38087 CTCGGTCGCACGACCTAATGGGCATCCCCCACACGAGCAATAAGAACGATCGAGCATCC
1 CTCGGTCGCACGGCCTAATGGGCATCCCCCACACGAGCAATAAGAACGATCGAGCATCC
* * *
38146 CTCGGTCGCACGGCGTAGTGGGCATCCCCCGCACGAGCAATAAGAACGATCGAGCATCC
1 CTCGGTCGCACGGCCTAATGGGCATCCCCCACACGAGCAATAAGAACGATCGAGCATCC
38205 CTCGGTCGCACGG
1 CTCGGTCGCACGG
38218 TACCCATTCA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.24, C:0.35, G:0.27, T:0.14
Consensus pattern (59 bp):
CTCGGTCGCACGGCCTAATGGGCATCCCCCACACGAGCAATAAGAACGATCGAGCATCC
Found at i:38920 original size:14 final size:16
Alignment explanation
Indices: 38901--38932 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
38891 TAATTAAATT
38901 AATAAAAT-GGTA-AA
1 AATAAAATAGGTATAA
38915 AATAAAATAGGTATAA
1 AATAAAATAGGTATAA
38931 AA
1 AA
38933 ATATTAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (16 bp):
AATAAAATAGGTATAA
Found at i:40070 original size:12 final size:12
Alignment explanation
Indices: 40053--40077 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40043 CAACACACTG
40053 AAAGTGGACCTC
1 AAAGTGGACCTC
40065 AAAGTGGACCTC
1 AAAGTGGACCTC
40077 A
1 A
40078 CTGAGTTGAC
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:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (12 bp):
AAAGTGGACCTC
Found at i:54411 original size:15 final size:15
Alignment explanation
Indices: 54391--54428 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
54381 ATAAATGACA
54391 CAAACCCGTTCTGTT
1 CAAACCCGTTCTGTT
54406 CAAACCCGTTCTGTT
1 CAAACCCGTTCTGTT
54421 CAAACCCG
1 CAAACCCG
54429 ACAAATCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.24, C:0.37, G:0.13, T:0.26
Consensus pattern (15 bp):
CAAACCCGTTCTGTT
Found at i:55876 original size:22 final size:21
Alignment explanation
Indices: 55851--55896 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
55841 TTTTTAGTTG
55851 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAA-TAAAAT
*
55873 AGTAAAATGGTAAAATAAAAT
1 AGTAAAATGATAAAATAAAAT
55894 AGT
1 AGT
55897 TATAAGGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.61, C:0.02, G:0.13, T:0.24
Consensus pattern (21 bp):
AGTAAAATGATAAAATAAAAT
Found at i:55948 original size:92 final size:93
Alignment explanation
Indices: 55774--55941 Score: 284
Period size: 92 Copynumber: 1.8 Consensus size: 93
55764 GCTTTTAAAT
* *
55774 TAAATTAGTAATATGGTAAAAATAAAATAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
*
55839 AGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGTTTTTAATTGAGTAAAACTATAAAAG
* *
55867 TAAAATAGTAAAATGGT-AAAATAAAATAGTTATAAGGATATTATATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
55931 AGTTTTTAATT
66 AGTTTTTAATT
55942 TTGTAAAGAA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
92 55 0.79
93 15 0.21
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (93 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAATTGAGTAAAACTATAAAAG
Found at i:55975 original size:27 final size:27
Alignment explanation
Indices: 55918--55975 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
55908 TATATTTAAT
* ***
55918 TAAATAAAAATAGAGTTTTTAATTTTG
1 TAAAGAAAAATAGAGTTTTTAATTGAC
* *
55945 TAAAGAAAAATAGTGTTTTTAGTTGAC
1 TAAAGAAAAATAGAGTTTTTAATTGAC
55972 TAAA
1 TAAA
55976 ACTATAAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.40
Consensus pattern (27 bp):
TAAAGAAAAATAGAGTTTTTAATTGAC
Found at i:56700 original size:5 final size:5
Alignment explanation
Indices: 56692--56741 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
56682 TATAGAATAG
56692 TAAGA TAAGA TAAGA T-AG- TAAGA TAAGATA TAAGA TAAAGA TAAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAG--A TAAGA T-AAGA T-AAGA
56739 TAA
1 TAA
56742 AGGTTTGCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
3 1 0.03
4 4 0.10
5 19 0.47
6 11 0.28
7 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.18, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:56715 original size:13 final size:12
Alignment explanation
Indices: 56696--56741 Score: 67
Period size: 13 Copynumber: 3.8 Consensus size: 12
56686 GAATAGTAAG
56696 ATAAGATAAGAT
1 ATAAGATAAGAT
56708 AGTAAGATAAGAT
1 A-TAAGATAAGAT
56721 ATAAGATAAAGAT
1 ATAAGAT-AAGAT
56734 A-AAGATAA
1 ATAAGATAA
56742 AGGTTTGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.06
12 12 0.38
13 18 0.56
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (12 bp):
ATAAGATAAGAT
Found at i:56732 original size:18 final size:19
Alignment explanation
Indices: 56688--56741 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
56678 TTTATATAGA
56688 ATAGTAAGAT-AAGATAAG
1 ATAGTAAGATAAAGATAAG
*
56706 ATAGTAAGATAAGATATAAG
1 ATAGTAAGATAA-AGATAAG
56726 ATA--AAGATAAAGATAA
1 ATAGTAAGATAAAGATAA
56742 AGGTTTGCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 17 0.53
19 1 0.03
20 9 0.28
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (19 bp):
ATAGTAAGATAAAGATAAG
Found at i:57725 original size:109 final size:109
Alignment explanation
Indices: 57534--57755 Score: 426
Period size: 109 Copynumber: 2.0 Consensus size: 109
57524 GGCCAATACA
57534 TATCTATATACTATATAAGTCTATACTTCAAAACCATTGACCTGAAATATCTAAAATAACCTTTT
1 TATCTATATACTATATAAGTCTATACTTCAAAACCATTGACCTGAAATATCTAAAATAACCTTTT
*
57599 TAATTTTAGAAGTTTAGTATTCATTTAAAGGGTAAACATGTATT
66 TAATTTTAGAAGTTTAGTATTCATTTAAAAGGTAAACATGTATT
*
57643 TATCTATATACTATATAAGTCTATACTTCAAAACCATTGACCTGAAATATCTAAAATAACTTTTT
1 TATCTATATACTATATAAGTCTATACTTCAAAACCATTGACCTGAAATATCTAAAATAACCTTTT
57708 TAATTTTAGAAGTTTAGTATTCATTTAAAAGGTAAACATGTATT
66 TAATTTTAGAAGTTTAGTATTCATTTAAAAGGTAAACATGTATT
57752 TATC
1 TATC
57756 AAATTACACT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 111 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (109 bp):
TATCTATATACTATATAAGTCTATACTTCAAAACCATTGACCTGAAATATCTAAAATAACCTTTT
TAATTTTAGAAGTTTAGTATTCATTTAAAAGGTAAACATGTATT
Found at i:57931 original size:39 final size:40
Alignment explanation
Indices: 57875--57955 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
57865 TTTAATTCCT
57875 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
57915 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
57954 AT
1 AT
57956 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:57983 original size:24 final size:25
Alignment explanation
Indices: 57946--57992 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
57936 AATACTTACA
57946 TTAATTAAATTC-TTAGGTATTTTT
1 TTAATTAAATTCTTTAGGTATTTTT
57970 TTAATTCAAA-TCTTTAGGTATTT
1 TTAATT-AAATTCTTTAGGTATTT
57993 GTGCAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
TTAATTAAATTCTTTAGGTATTTTT
Found at i:58301 original size:194 final size:189
Alignment explanation
Indices: 58064--58418 Score: 629
Period size: 194 Copynumber: 1.9 Consensus size: 189
58054 AACCTTAATA
58064 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
* * *
58129 ATTTAATAAATCAACCACTAATGTTTAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGT
66 ATTTAATAAATCAACCACTAATGTTCAACT-A-CTTTTTTGGTATAGTT-T-TATATATAATAAT
58194 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGACTTAAAAATTAATAACATTCACCATTG
127 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGACTTAAAAATTAATAACATTCACCATTG
*
58257 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTTAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
58322 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTGGTATAGTTTTATATATAATAATAAT
65 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTGGTATAGTTTTATATATAATAATAAT
58387 GTGTTGTATCTTATTCACTACAACTTTGTTAG
130 GTGTTGTATCTTATTCACTACAACTTTGTTAG
58419 TAATCTTAGA
Statistics
Matches: 157, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
190 47 0.30
191 1 0.01
192 15 0.10
193 17 0.11
194 77 0.49
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.46
Consensus pattern (189 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTGGTATAGTTTTATATATAATAATAATG
TGTTGTATCTTATTCACTACAACTTTGTTAGACTTAAAAATTAATAACATTCACCATTG
Found at i:59021 original size:35 final size:36
Alignment explanation
Indices: 58975--59043 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
58965 GAGATTTTGG
* *
58975 AGAAATATGATAATCAAAATTACAAAA-ATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAATA
59010 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAA
59044 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAGATGTAATA
Found at i:60424 original size:58 final size:58
Alignment explanation
Indices: 60323--60432 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
60313 ATCATGCCTC
* *
60323 GGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAATATGTCACTCGATAAGCTTT
1 GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCTTT
* * *
60381 GGTCCGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA
60433 TTTGATTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 30 0.65
59 16 0.35
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCTTT
Found at i:62447 original size:33 final size:33
Alignment explanation
Indices: 62395--62604 Score: 231
Period size: 33 Copynumber: 6.4 Consensus size: 33
62385 ATGGGATTAT
* * *
62395 TGGCGGCAGCAATGGTGGGGTTCGAGGCGTTGC
1 TGGCGGCGGCAATGGTGGGGTTTGAGGTGTTGC
* * * *
62428 TGGGGGCGGCAACGGTGGGGTTTGAGGGGTTGT
1 TGGCGGCGGCAATGGTGGGGTTTGAGGTGTTGC
* * *
62461 TGGCGGCGGCAACGGTGGGGTTTGAGGAGTTGT
1 TGGCGGCGGCAATGGTGGGGTTTGAGGTGTTGC
* *
62494 TGGCGGCAGCAATGGTGGGGTTTTAGGTGTTGC
1 TGGCGGCGGCAATGGTGGGGTTTGAGGTGTTGC
* * * * *
62527 TGGGGGCGGCAAAGGTGGAGTTTTAGGTGTTGT
1 TGGCGGCGGCAATGGTGGGGTTTGAGGTGTTGC
* * *
62560 TGGCGGCAGCAATGGTGGAGTTTTAGGTGTTGC
1 TGGCGGCGGCAATGGTGGGGTTTGAGGTGTTGC
*
62593 TGGGGGCGGCAA
1 TGGCGGCGGCAA
62605 AGGGGTTTCC
Statistics
Matches: 153, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 153 1.00
ACGTcount: A:0.13, C:0.12, G:0.50, T:0.26
Consensus pattern (33 bp):
TGGCGGCGGCAATGGTGGGGTTTGAGGTGTTGC
Found at i:62478 original size:66 final size:66
Alignment explanation
Indices: 62395--62607 Score: 264
Period size: 66 Copynumber: 3.2 Consensus size: 66
62385 ATGGGATTAT
* * * * * * * * * *
62395 TGGCGGCAGCAATGGTGGGGTTCGAGGCGTTGCTGGGGGCGGCAACGGTGGGGTTTGAGGGGTTG
1 TGGCGGCGGCAAAGGTGGGGTTTGAGGAGTTGTTGGCGGCAGCAATGGTGGGGTTTTAGGTGTTG
*
62460 T
66 C
*
62461 TGGCGGCGGCAACGGTGGGGTTTGAGGAGTTGTTGGCGGCAGCAATGGTGGGGTTTTAGGTGTTG
1 TGGCGGCGGCAAAGGTGGGGTTTGAGGAGTTGTTGGCGGCAGCAATGGTGGGGTTTTAGGTGTTG
62526 C
66 C
* * * * *
62527 TGGGGGCGGCAAAGGTGGAGTTTTAGGTGTTGTTGGCGGCAGCAATGGTGGAGTTTTAGGTGTTG
1 TGGCGGCGGCAAAGGTGGGGTTTGAGGAGTTGTTGGCGGCAGCAATGGTGGGGTTTTAGGTGTTG
62592 C
66 C
*
62593 TGGGGGCGGCAAAGG
1 TGGCGGCGGCAAAGG
62608 GGTTTCCGGC
Statistics
Matches: 130, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 130 1.00
ACGTcount: A:0.13, C:0.12, G:0.50, T:0.25
Consensus pattern (66 bp):
TGGCGGCGGCAAAGGTGGGGTTTGAGGAGTTGTTGGCGGCAGCAATGGTGGGGTTTTAGGTGTTG
C
Found at i:62544 original size:99 final size:99
Alignment explanation
Indices: 62394--62591 Score: 288
Period size: 99 Copynumber: 2.0 Consensus size: 99
62384 GATGGGATTA
* *
62394 TTGGCGGCAGCAATGGTGGGGTTCGAGGCGTTGCTGGGGGCGGCAACGGTGGGGTTTGAGGGGTT
1 TTGGCGGCAGCAATGGTGGGGTTCGAGGCGTTGCTGGGGGCGGCAAAGGTGGAGTTTGAGGGGTT
* *
62459 GTTGGCGGCGGCAACGGTGGGGTTTGAGGAGTTG
66 GTTGGCGGCAGCAACGGTGGAGTTTGAGGAGTTG
** * * *
62493 TTGGCGGCAGCAATGGTGGGGTTTTAGGTGTTGCTGGGGGCGGCAAAGGTGGAGTTTTAGGTGTT
1 TTGGCGGCAGCAATGGTGGGGTTCGAGGCGTTGCTGGGGGCGGCAAAGGTGGAGTTTGAGGGGTT
* * *
62558 GTTGGCGGCAGCAATGGTGGAGTTTTAGGTGTTG
66 GTTGGCGGCAGCAACGGTGGAGTTTGAGGAGTTG
62592 CTGGGGGCGG
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 87 1.00
ACGTcount: A:0.13, C:0.11, G:0.49, T:0.27
Consensus pattern (99 bp):
TTGGCGGCAGCAATGGTGGGGTTCGAGGCGTTGCTGGGGGCGGCAAAGGTGGAGTTTGAGGGGTT
GTTGGCGGCAGCAACGGTGGAGTTTGAGGAGTTG
Found at i:69641 original size:26 final size:27
Alignment explanation
Indices: 69589--69655 Score: 93
Period size: 26 Copynumber: 2.5 Consensus size: 27
69579 CAGACTCTGG
*
69589 ATTTTGAGTTTCGAACATGACAAGCAA
1 ATTTTGAGTTTTGAACATGACAAGCAA
69616 ATTTTGAGTTTTGAA-ATGA-AATGCAA
1 ATTTTGAGTTTTGAACATGACAA-GCAA
*
69642 ATTTTGAATTTTGA
1 ATTTTGAGTTTTGA
69656 CTTTTGAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 2 0.05
26 21 0.57
27 14 0.38
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (27 bp):
ATTTTGAGTTTTGAACATGACAAGCAA
Done.