Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018346.1 Corchorus olitorius cultivar O-4 contig18379, 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: 64089
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:532 original size:3 final size:3
Alignment explanation
Indices: 524--564 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
514 TTTTAATACA
524 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
565 ATATAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:607 original size:4 final size:4
Alignment explanation
Indices: 580--630 Score: 77
Period size: 4 Copynumber: 13.0 Consensus size: 4
570 ATAATATATA
* *
580 TATG TATA TATG TATG TATA TATG TATG TATG TATG TATG TATG TAT-
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
627 TATG
1 TATG
631 GCTCTAATCG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 3 0.07
4 39 0.93
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:626 original size:12 final size:12
Alignment explanation
Indices: 573--622 Score: 82
Period size: 12 Copynumber: 4.2 Consensus size: 12
563 ATATATAATA
*
573 ATATATATATGT
1 ATATATGTATGT
585 ATATATGTATGT
1 ATATATGTATGT
597 ATATATGTATGT
1 ATATATGTATGT
*
609 ATGTATGTATGT
1 ATATATGTATGT
621 AT
1 AT
623 GTATTATGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (12 bp):
ATATATGTATGT
Found at i:771 original size:3 final size:3
Alignment explanation
Indices: 763--788 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
753 TCAAAGACGA
763 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
789 AAATAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1746 original size:25 final size:24
Alignment explanation
Indices: 1718--1772 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
1708 TTAATATTCA
* *
1718 AAATTAATATATAAAGGGACTAAAT
1 AAATTAACA-ATAAAGAGACTAAAT
* *
1743 AAATCTAACAATAAAGATATTAAAT
1 AAAT-TAACAATAAAGAGACTAAAT
1768 AAATT
1 AAATT
1773 TAAGAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 20 0.80
26 4 0.16
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.29
Consensus pattern (24 bp):
AAATTAACAATAAAGAGACTAAAT
Found at i:4189 original size:22 final size:22
Alignment explanation
Indices: 4147--4189 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4137 AAGTTTTTTT
* *
4147 AATTAAATTTGTAAAATGATAA
1 AATTAAAATTGTAAAAGGATAA
*
4169 AATTAAAATTGTATAAGGATA
1 AATTAAAATTGTAAAAGGATA
4190 TTAGATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (22 bp):
AATTAAAATTGTAAAAGGATAA
Found at i:4276 original size:92 final size:91
Alignment explanation
Indices: 4159--4334 Score: 291
Period size: 92 Copynumber: 1.9 Consensus size: 91
4149 TTAAATTTGT
*
4159 AAAATGATAAAATTAAAATTGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAAT
1 AAAATGATAAAATTAAAATTGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAAT
4224 TGAGTAAAACTATAAAAGTATATTTA
66 TGAGTAAAACTATAAAAGTATATTTA
*
4250 AAAATGGTAAAAATTAAATATT-TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA
1 AAAATGAT-AAAATTAAA-ATTGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA
* *
4314 GTTGAGTAAAATTATAAAAGT
64 ATTGAGTAAAACTATAAAAGT
4335 TTAAACAATG
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
91 7 0.09
92 69 0.87
93 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.36
Consensus pattern (91 bp):
AAAATGATAAAATTAAAATTGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAAT
TGAGTAAAACTATAAAAGTATATTTA
Found at i:4998 original size:15 final size:15
Alignment explanation
Indices: 4978--5006 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4968 TGCTTCTATC
4978 TATACTATATCAATT
1 TATACTATATCAATT
4993 TATACTATATCAAT
1 TATACTATATCAAT
5007 CGCCATGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (15 bp):
TATACTATATCAATT
Found at i:6655 original size:60 final size:60
Alignment explanation
Indices: 6506--6655 Score: 187
Period size: 60 Copynumber: 2.5 Consensus size: 60
6496 AATTAATTTA
* * * *
6506 AGCATTTATGCATATGTTGAGGG-CCTATTTAACAAAATTCAAAGCATGGACCCTCAATTG
1 AGCATTTTTGCATATGTT-AGGGACCTATTTAACAAAACTAAAAGCATGGACCCTAAATTG
** * *
6566 AGCATTTTTGCATACATTA-GAAGCCTATTTAACCAAACTAAAAGCATGGACCCTAAATTG
1 AGCATTTTTGCATATGTTAGGGA-CCTATTTAACAAAACTAAAAGCATGGACCCTAAATTG
*
6626 AGCATTTTTGCATATGTTAGGGACTTATTT
1 AGCATTTTTGCATATGTTAGGGACCTATTT
6656 GAATAATTAG
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 71 0.95
61 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (60 bp):
AGCATTTTTGCATATGTTAGGGACCTATTTAACAAAACTAAAAGCATGGACCCTAAATTG
Found at i:7415 original size:16 final size:16
Alignment explanation
Indices: 7390--7420 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7380 ATATATATCT
7390 AATTTATTAAATTAAA
1 AATTTATTAAATTAAA
*
7406 AATTTTTTAAATTAA
1 AATTTATTAAATTAA
7421 TTTTTTTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTATTAAATTAAA
Found at i:7635 original size:60 final size:60
Alignment explanation
Indices: 7558--7700 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 60
7548 TGTACAAGAC
* * *
7558 TTTGCACAAAACTTAATAGTACATGGATAC-ATATCACCCAAATTTTTAAACTAGGACTTA
1 TTTGCACAATACTTAATAGTACATGGA-ACTATATCACACAAATTTTTAAACAAGGACTTA
* * * ** ** *
7618 TTTGCACAATACCTAATAGTATATGGACCTATATCACATGAATTTTTGTACAAGGACTTT
1 TTTGCACAATACTTAATAGTACATGGAACTATATCACACAAATTTTTAAACAAGGACTTA
*
7678 TTTGCTCAATACTTAATAGTACA
1 TTTGCACAATACTTAATAGTACA
7701 GGGACCTACG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 1 0.01
60 67 0.99
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (60 bp):
TTTGCACAATACTTAATAGTACATGGAACTATATCACACAAATTTTTAAACAAGGACTTA
Found at i:21794 original size:125 final size:128
Alignment explanation
Indices: 21609--21869 Score: 429
Period size: 131 Copynumber: 2.0 Consensus size: 128
21599 TTTGTCTCGT
21609 GAAACCATGTGACCATTTTCCTTTTTTGGATAAAATATCATATTACCATTTTCAGCCGAAGAGAA
1 GAAACCATGTGACCATTTTCCTTTTTTGGATAAAATATCATATTACCATTTTCAGCCGAAGAGAA
*
21674 TATAAG-AA-AGATTTCAAATTTTGATCAAACATACAAGTACTAACTTTGCATTTCTAAATAA
66 TATAAGAAATAGATTTCAAACTTTGATCAAACATACAAGTACTAACTTTGCATTTCTAAATAA
* *
21735 GAAACCATGTTACCATTTTCCTTTTTTGGAT-AAATATCATTTTACCATTTTCAGCCGAAGAGAA
1 GAAACCATGTGACCATTTTCCTTTTTTGGATAAAATATCATATTACCATTTTCAGCCGAAGAGAA
21799 TATAAGAAAATTTCAGATTTCAAACTTTGATCAAACATACAAGTACTAACTTTGCATTTCTAAAT
66 TATAAG-AAA--T-AGATTTCAAACTTTGATCAAACATACAAGTACTAACTTTGCATTTCTAAAT
*
21864 AG
127 AA
21866 GAAA
1 GAAA
21870 TAACATTTGA
Statistics
Matches: 125, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
125 38 0.30
126 30 0.24
127 2 0.02
131 55 0.44
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (128 bp):
GAAACCATGTGACCATTTTCCTTTTTTGGATAAAATATCATATTACCATTTTCAGCCGAAGAGAA
TATAAGAAATAGATTTCAAACTTTGATCAAACATACAAGTACTAACTTTGCATTTCTAAATAA
Found at i:23461 original size:38 final size:38
Alignment explanation
Indices: 23386--23461 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
23376 CAGCACCATC
* * *
23386 CCATATAATAAGTTTTCAAAGCCACTTAGAGGTGCCTT
1 CCATATAATAAGTTTTCAAAGCCACTAAAAGGAGCCTT
*
23424 CCATATAATAAGTTTTCAAAGCCACTAAAATGAGCCTT
1 CCATATAATAAGTTTTCAAAGCCACTAAAAGGAGCCTT
23462 AACTCAGCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (38 bp):
CCATATAATAAGTTTTCAAAGCCACTAAAAGGAGCCTT
Found at i:31313 original size:10 final size:9
Alignment explanation
Indices: 31288--31312 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
31278 AACAATAAGG
31288 AAAAAAAGA
1 AAAAAAAGA
31297 AAAAAAAGA
1 AAAAAAAGA
31306 AAAAAAA
1 AAAAAAA
31313 AAGAAGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:32909 original size:7 final size:7
Alignment explanation
Indices: 32897--32930 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
32887 TCTTCATTAA
32897 TTCCTTC
1 TTCCTTC
32904 TTCCTTC
1 TTCCTTC
32911 TTCCTTC
1 TTCCTTC
*
32918 TTCTTCTC
1 TTCCT-TC
32926 TTCCT
1 TTCCT
32931 GACTTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
TTCCTTC
Found at i:37049 original size:25 final size:25
Alignment explanation
Indices: 37021--37070 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
37011 TTTTGTTATC
*
37021 CAATTTTTTATGCACTTGAATTAAA
1 CAATTTTGTATGCACTTGAATTAAA
37046 CAATTTTGTATGCACTTGAATTAAA
1 CAATTTTGTATGCACTTGAATTAAA
37071 TTATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (25 bp):
CAATTTTGTATGCACTTGAATTAAA
Found at i:41312 original size:10 final size:10
Alignment explanation
Indices: 41297--41369 Score: 64
Period size: 10 Copynumber: 7.3 Consensus size: 10
41287 AGTGTCGTCA
41297 GCGCGTGGCG
1 GCGCGTGGCG
*
41307 GCGCGT-GTG
1 GCGCGTGGCG
*
41316 GTGCGTGGGCG
1 GCGCGT-GGCG
41327 GCGCGTGGACG
1 GCGCGTGG-CG
41338 GCGCGT-GCG
1 GCGCGTGGCG
41347 AGCGCGTGAG-G
1 -GCGCGTG-GCG
41358 GCGCGT-GCG
1 GCGCGTGGCG
41367 GCG
1 GCG
41370 TCCTTTTGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
8 1 0.02
9 13 0.25
10 21 0.40
11 16 0.31
12 1 0.02
ACGTcount: A:0.04, C:0.26, G:0.58, T:0.12
Consensus pattern (10 bp):
GCGCGTGGCG
Found at i:41362 original size:20 final size:19
Alignment explanation
Indices: 41297--41369 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
41287 AGTGTCGTCA
*
41297 GCGCGTGGCGGCGCGTGTGG
1 GCGCGT-GCGGCGCGTGAGG
* * *
41317 TGCGTGGGCGGCGCGTGGACG
1 -GCGCGTGCGGCGCGT-GAGG
41338 GCGCGTGCGAGCGCGTGAGG
1 GCGCGTGCG-GCGCGTGAGG
41358 GCGCGTGCGGCG
1 GCGCGTGCGGCG
41370 TCCTTTTGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 3 0.07
20 28 0.65
21 12 0.28
ACGTcount: A:0.04, C:0.26, G:0.58, T:0.12
Consensus pattern (19 bp):
GCGCGTGCGGCGCGTGAGG
Found at i:47020 original size:16 final size:16
Alignment explanation
Indices: 46999--47056 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
46989 TGGCCACCTT
*
46999 TTTTTTAATTGCTTAA
1 TTTTTTAATTACTTAA
* **
47015 TTTTTTAATTTCGAAA
1 TTTTTTAATTACTTAA
47031 TTTTTGTAATTACTTAA
1 TTTTT-TAATTACTTAA
47048 -TTTTTAATT
1 TTTTTTAATT
47057 TAAAAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 5 0.14
16 22 0.63
17 8 0.23
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTTAATTACTTAA
Found at i:47020 original size:17 final size:17
Alignment explanation
Indices: 46998--47052 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
46988 ATGGCCACCT
*
46998 TTTTTTTAATTGCTTAA
1 TTTTTTTAATTACTTAA
* **
47015 -TTTTTTAATTTCGAAA
1 TTTTTTTAATTACTTAA
*
47031 TTTTTGTAATTACTTAA
1 TTTTTTTAATTACTTAA
47048 TTTTT
1 TTTTT
47053 AATTTAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 13 0.43
17 17 0.57
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.64
Consensus pattern (17 bp):
TTTTTTTAATTACTTAA
Found at i:47066 original size:33 final size:33
Alignment explanation
Indices: 46998--47062 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
46988 ATGGCCACCT
* * **
46998 TTTTTTTAATTGCTTAATTTTTTAATTTCGAAA
1 TTTTTGTAATTACTTAATTTTTTAATTTAAAAA
47031 TTTTTGTAATTACTTAA-TTTTTAATTTAAAAA
1 TTTTTGTAATTACTTAATTTTTTAATTTAAAAA
47063 ATTTCCAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (33 bp):
TTTTTGTAATTACTTAATTTTTTAATTTAAAAA
Found at i:48658 original size:32 final size:32
Alignment explanation
Indices: 48617--48677 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
48607 AAATATGTTT
*
48617 GAAAAATAAGGGTATAATGGTCGATTCAATTA
1 GAAAAATAAGGGTATAATAGTCGATTCAATTA
48649 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGGTATAATAGTCGATTCAA
48678 AAGTTTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGGTATAATAGTCGATTCAATTA
Found at i:49948 original size:16 final size:15
Alignment explanation
Indices: 49911--49996 Score: 82
Period size: 16 Copynumber: 5.5 Consensus size: 15
49901 GTTTTCTCGG
* *
49911 GTCATTTGGGTTCGG
1 GTCATTCGGGTTCGA
*
49926 GTTATTCGGGCTTCGA
1 GTCATTCGGG-TTCGA
*
49942 GTCATTCGGGTTCCGG
1 GTCATTCGGGTT-CGA
49958 GTCATTCGGGTCTCGA
1 GTCATTCGGGT-TCGA
* *
49974 GTCATTTGGGTTCCGG
1 GTCATTCGGGTT-CGA
49990 GTCATTC
1 GTCATTC
49997 AGGTCTACCG
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
15 11 0.19
16 46 0.79
17 1 0.02
ACGTcount: A:0.09, C:0.21, G:0.34, T:0.36
Consensus pattern (15 bp):
GTCATTCGGGTTCGA
Found at i:49965 original size:32 final size:32
Alignment explanation
Indices: 49905--50002 Score: 137
Period size: 32 Copynumber: 3.1 Consensus size: 32
49895 CAGACAGTTT
* *
49905 TCTCGGGTCATTTGGGTT-CGGGTTATTCGGG
1 TCTCGAGTCATTTGGGTTCCGGGTCATTCGGG
*
49936 -CTTCGAGTCATTCGGGTTCCGGGTCATTCGGG
1 TC-TCGAGTCATTTGGGTTCCGGGTCATTCGGG
*
49968 TCTCGAGTCATTTGGGTTCCGGGTCATTCAGG
1 TCTCGAGTCATTTGGGTTCCGGGTCATTCGGG
50000 TCT
1 TCT
50003 ACCGGGTCTC
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.02
31 14 0.24
32 43 0.73
33 1 0.02
ACGTcount: A:0.09, C:0.21, G:0.34, T:0.36
Consensus pattern (32 bp):
TCTCGAGTCATTTGGGTTCCGGGTCATTCGGG
Found at i:50266 original size:42 final size:42
Alignment explanation
Indices: 50219--50300 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
50209 TAGATATTAA
*
50219 TTTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
50261 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
50301 TGTGTTAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:52994 original size:12 final size:12
Alignment explanation
Indices: 52974--53006 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
52964 GCCCGAGCCC
52974 AACCCGAAACCG
1 AACCCGAAACCG
*
52986 AACCTGAAACCG
1 AACCCGAAACCG
52998 AACCCGAAA
1 AACCCGAAA
53007 ATACCCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.36, G:0.15, T:0.03
Consensus pattern (12 bp):
AACCCGAAACCG
Found at i:53065 original size:16 final size:16
Alignment explanation
Indices: 53009--53097 Score: 67
Period size: 16 Copynumber: 5.6 Consensus size: 16
52999 ACCCGAAAAT
*
53009 ACCCAAACCCAACATA
1 ACCCAAACCCAACAGA
**
53025 ACCTGAACCCGAA-A-A
1 ACCCAAACCC-AACAGA
*
53040 TACTCAAACCCAACAGA
1 -ACCCAAACCCAACAGA
* *
53057 ACCCGAACCCGAA-AAA
1 ACCCAAACCC-AACAGA
*
53073 ACCCAAACCCGACAGA
1 ACCCAAACCCAACAGA
53089 ACCCAAACC
1 ACCCAAACC
53098 TGAAGTGACC
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
15 4 0.07
16 47 0.84
17 5 0.09
ACGTcount: A:0.47, C:0.40, G:0.08, T:0.04
Consensus pattern (16 bp):
ACCCAAACCCAACAGA
Found at i:53092 original size:32 final size:32
Alignment explanation
Indices: 52995--53097 Score: 152
Period size: 32 Copynumber: 3.2 Consensus size: 32
52985 GAACCTGAAA
*
52995 CCGAACCCGAAAATACCCAAACCCAACATAAC
1 CCGAACCCGAAAATACCCAAACCCAACAGAAC
* *
53027 CTGAACCCGAAAATACTCAAACCCAACAGAAC
1 CCGAACCCGAAAATACCCAAACCCAACAGAAC
* *
53059 CCGAACCCGAAAAAACCCAAACCCGACAGAAC
1 CCGAACCCGAAAATACCCAAACCCAACAGAAC
*
53091 CCAAACC
1 CCGAACC
53098 TGAAGTGACC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.47, C:0.40, G:0.09, T:0.05
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCAAACCCAACAGAAC
Found at i:59299 original size:16 final size:15
Alignment explanation
Indices: 59278--59320 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
59268 TTACTCTACT
59278 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
59294 TTGTTTTTCTGTTTAA
1 TTG-TTTTCTGTTTAA
59310 TTGTTTTCTGT
1 TTGTTTTCTGT
59321 CAACCTCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.31
16 12 0.46
17 6 0.23
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:59827 original size:49 final size:50
Alignment explanation
Indices: 59732--59828 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 50
59722 CGTTTTTTCT
* * * *
59732 AAAAAAATATTTTTTGCGTCATAAAAAAAATTGTTTTGTGTTTTGCGTCG
1 AAAAAAATAATTTCTGCGTCATAAAAAAAATTGTCTTGTGTCTTGCGTCG
59782 AAAAAAA-AATTTCTGCGTCATAAAAAAAAAATT-TCTTGT-TCTTGCGT
1 AAAAAAATAATTTCTGCGTCAT--AAAAAAAATTGTCTTGTGTCTTGCGT
59829 TTTTAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 19 0.46
50 12 0.29
51 10 0.24
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (50 bp):
AAAAAAATAATTTCTGCGTCATAAAAAAAATTGTCTTGTGTCTTGCGTCG
Found at i:62186 original size:21 final size:21
Alignment explanation
Indices: 62162--62211 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
62152 GCAGCATTTT
**
62162 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
62183 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
62204 CCGTGCCA
1 CCGTGCCA
62212 TCACGATTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Done.