Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016033.1 Corchorus capsularis cultivar CVL-1 contig16054, 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: 53888
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1739 original size:31 final size:30
Alignment explanation
Indices: 1702--1801 Score: 148
Period size: 31 Copynumber: 3.3 Consensus size: 30
1692 AGGGGCTAAA
1702 TGCTCAATTTGGTCCTAAACCTTTGAGCGAG
1 TGCTCAATTTGGTCCTAAACCTTTGAGCG-G
* *
1733 TGCTCAATTTGGTCCTAAACCTTTGAAC-C
1 TGCTCAATTTGGTCCTAAACCTTTGAGCGG
*
1762 TGCTCAATTTGGTTCTAAACCTTTGAGCGG
1 TGCTCAATTTGGTCCTAAACCTTTGAGCGG
1792 TTGCTCAATT
1 -TGCTCAATT
1802 CAGTCCTATT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
29 26 0.42
31 36 0.58
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (30 bp):
TGCTCAATTTGGTCCTAAACCTTTGAGCGG
Found at i:5399 original size:31 final size:30
Alignment explanation
Indices: 5318--5414 Score: 135
Period size: 31 Copynumber: 3.2 Consensus size: 30
5308 TAAGACTGAC
5318 TTGAGCGACCGCTCAAAGGTTTAGGACCAAA
1 TTGAGCG-CCGCTCAAAGGTTTAGGACCAAA
* *
5349 TTGAGCAG--GTTTAAAGGTTTAGGACCAAA
1 TTGAGC-GCCGCTCAAAGGTTTAGGACCAAA
5378 TTGAGCGCTCGCTCAAAGGTTTAGGACCAAA
1 TTGAGCGC-CGCTCAAAGGTTTAGGACCAAA
5409 TTGAGC
1 TTGAGC
5415 ATTTAGCCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.02
29 25 0.43
31 31 0.53
32 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (30 bp):
TTGAGCGCCGCTCAAAGGTTTAGGACCAAA
Found at i:9970 original size:31 final size:31
Alignment explanation
Indices: 9935--9993 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
9925 ATGTTTTCCG
*
9935 ATTGTACCCTTATT-TATAAAACATATTTTCA
1 ATTGTACCATT-TTCTATAAAACATATTTTCA
*
9966 ATTGTACCATTTTCTTTAAAACATATTT
1 ATTGTACCATTTTCTATAAAACATATTT
9994 CTAAATTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTGTACCATTTTCTATAAAACATATTTTCA
Found at i:10159 original size:38 final size:35
Alignment explanation
Indices: 10094--10170 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 35
10084 AATTTGGCTT
10094 TTTGTTTCCAACGTCCTATTTAATTTTGTCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTG-C-TTTGTC
** *
10131 TTTGTTTCCAATCGTTGTATTTGATTTTGCTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCTTTGTC
10167 TTTG
1 TTTG
10171 GTCTTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 10 0.28
37 12 0.33
38 14 0.39
ACGTcount: A:0.12, C:0.16, G:0.14, T:0.58
Consensus pattern (35 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTGTC
Found at i:10334 original size:19 final size:20
Alignment explanation
Indices: 10307--10345 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10297 TACTATTATT
10307 TTTTGAATTT-AATATTTTAA
1 TTTTGAATTTCAAT-TTTTAA
10327 TTTT-AATTTCAATTTTTAA
1 TTTTGAATTTCAATTTTTAA
10346 ATGTCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAA
Found at i:10566 original size:22 final size:21
Alignment explanation
Indices: 10512--10596 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 21
10502 CTCTATGTGA
*
10512 TTATCAAAATTTCATAAGATGG
1 TTATCAAAATTTCATAGGA-GG
* *
10534 TTATTATAATTTCATGAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
10556 TTATCAAAATTCCATAGTGTA-G
1 TTATCAAAATTTCATAG-G-AGG
*
10578 TTACCAAAATTTCATAGGA
1 TTATCAAAATTTCATAGGA
10597 TCAGGTTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 3 0.06
22 44 0.85
23 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:10866 original size:22 final size:22
Alignment explanation
Indices: 10814--11067 Score: 120
Period size: 22 Copynumber: 11.5 Consensus size: 22
10804 TAAGGAGTAC
*
10814 CAAAATTTGATAGAAG-G-TTAT
1 CAAAATTTCATA-AAGTGATTAT
*
10835 C-AAATCTCATAAAGTGATTAT
1 CAAAATTTCATAAAGTGATTAT
* *
10856 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAAAG-T--GATTAT
*
10881 CAAAATTT-ATAGAA-AGATTAT
1 CAAAATTTCATA-AAGTGATTAT
**
10902 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAAAG-TGATTAT
*
10924 CAAAATTTC--AAAGCGAGGTTAT
1 CAAAATTTCATAAAGTGA--TTAT
* * * *
10946 CGAAATTACATAATGCGATTAT
1 CAAAATTTCATAAAGTGATTAT
* * * * * *
10968 CAGAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAAAGTGATTAT
* *
10990 CAAAATATT-ATAAAGAGGTTAT
1 CAAAAT-TTCATAAAGTGATTAT
11012 CAAAATTTCATAAAGATG-TTAT
1 CAAAATTTCATAAAG-TGATTAT
11034 C-AAATTTCCA-AAATGTGATTA-
1 CAAAATTT-CATAAA-GTGATTAT
11055 CAAAAATTTCATA
1 C-AAAATTTCATA
11068 TTGGTATTTC
Statistics
Matches: 178, Mismatches: 31, Indels: 46
0.70 0.12 0.18
Matches are distributed among these distances:
19 4 0.02
20 11 0.06
21 34 0.19
22 94 0.53
23 12 0.07
24 9 0.05
25 14 0.08
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAAAGTGATTAT
Found at i:10886 original size:25 final size:22
Alignment explanation
Indices: 10814--10914 Score: 84
Period size: 21 Copynumber: 4.6 Consensus size: 22
10804 TAAGGAGTAC
* *
10814 CAAAATTTGATAG-AAGGTTAT
1 CAAAATTTCATAGAAAGATTAT
* *
10835 C-AAATCTCATA-AAGTGATTAT
1 CAAAATTTCATAGAA-AGATTAT
* *
10856 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGA-A--AGATTAT
10881 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAAAGATTAT
10902 CAAAATTTCATAG
1 CAAAATTTCATAG
10915 TGTTGTTATC
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
20 9 0.14
21 21 0.33
22 13 0.20
23 2 0.03
24 6 0.09
25 13 0.20
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGATTAT
Found at i:11175 original size:20 final size:20
Alignment explanation
Indices: 11150--11200 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
11140 TTATGGAGTA
11150 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
11170 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
*
11189 ATAAAAATTTCA
1 ATCAAAATTTCA
11201 TATGAAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAGGGAGGAT
Found at i:11259 original size:22 final size:22
Alignment explanation
Indices: 11234--11726 Score: 224
Period size: 22 Copynumber: 22.6 Consensus size: 22
11224 TGTTTAGTTT
*
11234 TCAAAATTTCATA-AGACGGTTA
1 TCAAAATTTCATAGGGA-GGTTA
* * * *
11256 TCAAAATTTCACA-GTATGTAGA
1 TCAAAATTTCATAGGGAGGT-TA
*
11278 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAGGGAGGTTA
*
11300 ACAAAATTTCATAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
** *
11322 TCAAAAAATCATAGGGAGCTTA
1 TCAAAATTTCATAGGGAGGTTA
11344 TCAAAAATTT--TA---A--TTA
1 TC-AAAATTTCATAGGGAGGTTA
* * * *
11360 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATAGGGAGGTTA
*
11382 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATAGGGAGG-TTA
* * *
11405 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAGGGAG-GTTA
*
11428 TCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
11450 TCACAATTTCATAGTGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
11472 TCAAAATTTCAGAGTGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
11494 -CTAACAA-TTCATATGAAGGTTT
1 TC-AA-AATTTCATAGGGAGGTTA
* * ** *
11516 TTAAATTTTCATAACGTGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
11538 TCAATATATCATATGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * **
11560 TCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATAG-GGAGGTTA
**
11583 TCAAAATTTCATATTGAGGTCT-
1 TCAAAATTTCATAGGGAGGT-TA
* *
11605 TCAAAATTCCTTAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
11627 ACCAAATTTCATAAGAAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
** ** * *
11649 AAAAAATTT-AT-GAAAAGATTC
1 TCAAAATTTCATAG-GGAGGTTA
* * * *
11670 TCGAAATTCCATA-GTATCGTTA
1 TCAAAATTTCATAGGGA-GGTTA
* *
11692 TCAAAATTTCATAGGAAGTTTA
1 TCAAAATTTCATAGGGAGGTTA
11714 TCAAAATTTCATA
1 TCAAAATTTCATA
11727 ATGGGATCAT
Statistics
Matches: 349, Mismatches: 98, Indels: 48
0.71 0.20 0.10
Matches are distributed among these distances:
15 6 0.02
16 5 0.01
17 2 0.01
18 1 0.00
20 1 0.00
21 20 0.06
22 246 0.70
23 68 0.19
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAGGGAGGTTA
Found at i:11875 original size:3 final size:3
Alignment explanation
Indices: 11867--11911 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
11857 ACAGATATAT
11867 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11912 CCCACTCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:14747 original size:21 final size:20
Alignment explanation
Indices: 14707--14748 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
14697 GTTTCAACCC
14707 TTGAGTTTGTGGCTGCTTTTG
1 TTGAGTTTGTGGCT-CTTTTG
14728 TTGAGGTTTGCTGGCT-TTTTG
1 TTGA-GTTTG-TGGCTCTTTTG
14749 GCTTGGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.05, C:0.10, G:0.33, T:0.52
Consensus pattern (20 bp):
TTGAGTTTGTGGCTCTTTTG
Found at i:22152 original size:20 final size:20
Alignment explanation
Indices: 22127--22168 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
22117 GCGGACACTC
*
22127 AAGTCGTTGCGTTAGATCTT
1 AAGTCGTTGCGTTAGATATT
22147 AAGTCGTTGCGTTAGATATT
1 AAGTCGTTGCGTTAGATATT
22167 AA
1 AA
22169 ACAACGGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (20 bp):
AAGTCGTTGCGTTAGATATT
Found at i:26859 original size:38 final size:37
Alignment explanation
Indices: 26811--26882 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
26801 CTTGGTCAAT
* ** *
26811 ATACATGTCTTTTCGTATAGACATAACTTTTATGATCA
1 ATACATGTCTTTCCAAACAGACATAAC-TTTATGATCA
26849 ATACATGTCTTTCCAAACAGACATAACTTTATGA
1 ATACATGTCTTTCCAAACAGACATAACTTTATGA
26883 ATAATTATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 7 0.23
38 23 0.77
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAACAGACATAACTTTATGATCA
Found at i:27907 original size:5 final size:5
Alignment explanation
Indices: 27857--27904 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
27847 AACCATCATC
* * *
27857 ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCCA ATCCA ATCCA ATC
1 ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATC
27905 CAACCCCATC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (5 bp):
ATCTA
Found at i:32734 original size:22 final size:22
Alignment explanation
Indices: 32706--32750 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
32696 CTCGCCTAGA
* *
32706 ATTTTTCGAATCGATCTCGAGT
1 ATTTTTCGAATCGAACCCGAGT
*
32728 ATTTTTCGAGTCGAACCCGAGT
1 ATTTTTCGAATCGAACCCGAGT
32750 A
1 A
32751 ACTTGCGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (22 bp):
ATTTTTCGAATCGAACCCGAGT
Found at i:32858 original size:27 final size:27
Alignment explanation
Indices: 32820--32874 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
32810 AATTCCATCT
32820 ATCATTCATAATGAAAGTTAATAATAA
1 ATCATTCATAATGAAAGTTAATAATAA
32847 ATCATTCATAATGAAAGTTAATAATAA
1 ATCATTCATAATGAAAGTTAATAATAA
32874 A
1 A
32875 CAGGTTTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (27 bp):
ATCATTCATAATGAAAGTTAATAATAA
Found at i:33092 original size:5 final size:5
Alignment explanation
Indices: 33082--33110 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
33072 TGGGGCAGAG
33082 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
33111 ATGAGGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:42631 original size:16 final size:17
Alignment explanation
Indices: 42611--42654 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
42601 GTTTGGCATC
42611 GTTTTCGTTTTTCTGTT
1 GTTTTCGTTTTTCTGTT
* * *
42628 -TTTTTGTTTTTGTTTT
1 GTTTTCGTTTTTCTGTT
42644 GTTTTCGTTTT
1 GTTTTCGTTTT
42655 GTTTTTGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.00, C:0.07, G:0.16, T:0.77
Consensus pattern (17 bp):
GTTTTCGTTTTTCTGTT
Found at i:42643 original size:11 final size:11
Alignment explanation
Indices: 42629--42663 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
42619 TTTTCTGTTT
42629 TTTTGTTTTTG
1 TTTTGTTTTTG
*
42640 TTTTGTTTTCG
1 TTTTGTTTTTG
42651 TTTTGTTTTTG
1 TTTTGTTTTTG
42662 TT
1 TT
42664 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:45963 original size:15 final size:16
Alignment explanation
Indices: 45930--45987 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
45920 CGGGTTCGGG
45930 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
45946 CGGGTTCGGGTA-TTT
1 CGGGTTCGGGTATTTT
*
45961 CGGGTTCGAGTATTTT
1 CGGGTTCGGGTATTTT
*
45977 CGGATTCGGGT
1 CGGGTTCGGGT
45988 TCGGATCGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 14 0.37
16 24 0.63
ACGTcount: A:0.09, C:0.14, G:0.38, T:0.40
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:46001 original size:17 final size:17
Alignment explanation
Indices: 45976--46023 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
45966 TCGAGTATTT
*
45976 TCGGATTCGGGTTCGGA
1 TCGGGTTCGGGTTCGGA
** *
45993 TCGGGTTCGGGCCCGGG
1 TCGGGTTCGGGTTCGGA
46010 TCGGGTTCGGGTTC
1 TCGGGTTCGGGTTC
46024 AGTTTCAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.04, C:0.23, G:0.46, T:0.27
Consensus pattern (17 bp):
TCGGGTTCGGGTTCGGA
Found at i:48475 original size:21 final size:21
Alignment explanation
Indices: 48449--48493 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
48439 ATAAACTGGA
48449 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
48470 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
48491 TTG
1 TTG
48494 ACGTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:48738 original size:32 final size:32
Alignment explanation
Indices: 48693--48760 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
48683 CCAAGAGGGC
*
48693 GGCTTACCGTGGCGAAGCCGCCCCACTGGGGA
1 GGCTTACCATGGCGAAGCCGCCCCACTGGGGA
48725 GGCTTACCATGGCGAAGCCGCCCCACTGGGGA
1 GGCTTACCATGGCGAAGCCGCCCCACTGGGGA
48757 GGCT
1 GGCT
48761 CCGCCGTGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.16, C:0.34, G:0.37, T:0.13
Consensus pattern (32 bp):
GGCTTACCATGGCGAAGCCGCCCCACTGGGGA
Found at i:48793 original size:33 final size:33
Alignment explanation
Indices: 48751--48826 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
48741 GCCGCCCCAC
*
48751 TGGGGAGGCTCCGCCGTGGTTGAGCC-TCCCTAG
1 TGGGGAGGCTCCGCCGTGGCTGAGCCGT-CCTAG
48784 TGGGGAGGCTCCGCCGTGGCTGAGCCGTCCTAG
1 TGGGGAGGCTCCGCCGTGGCTGAGCCGTCCTAG
48817 TGGGGAGGCT
1 TGGGGAGGCT
48827 AGTGTAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 40 0.98
34 1 0.02
ACGTcount: A:0.09, C:0.28, G:0.43, T:0.20
Consensus pattern (33 bp):
TGGGGAGGCTCCGCCGTGGCTGAGCCGTCCTAG
Found at i:48802 original size:16 final size:16
Alignment explanation
Indices: 48751--48802 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
48741 GCCGCCCCAC
48751 TGGGGAGGCTCCGCCG
1 TGGGGAGGCTCCGCCG
* * *
48767 TGGTTGAGCCTCC-CTAG
1 TGG-GGAGGCTCCGC-CG
48784 TGGGGAGGCTCCGCCG
1 TGGGGAGGCTCCGCCG
48800 TGG
1 TGG
48803 CTGAGCCGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.08, C:0.29, G:0.44, T:0.19
Consensus pattern (16 bp):
TGGGGAGGCTCCGCCG
Done.