Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009719.1 Corchorus capsularis cultivar CVL-1 contig09740, 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: 47688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:371 original size:19 final size:19
Alignment explanation
Indices: 349--405 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
339 TTAATTCAGG
349 GTAATTAAGTGAGTCAGTA
1 GTAATTAAGTGAGTCAGTA
* * * * *
368 GTAATCAACTTAATTCAG-G
1 GTAATTAA-GTGAGTCAGTA
387 GTAATTAAGTGAGTCAGTA
1 GTAATTAAGTGAGTCAGTA
406 ATCAACTTAA
Statistics
Matches: 26, Mismatches: 10, Indels: 4
0.65 0.25 0.10
Matches are distributed among these distances:
18 6 0.23
19 14 0.54
20 6 0.23
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.32
Consensus pattern (19 bp):
GTAATTAAGTGAGTCAGTA
Found at i:413 original size:35 final size:35
Alignment explanation
Indices: 329--500 Score: 292
Period size: 35 Copynumber: 4.8 Consensus size: 35
319 GTGAGTCAGT
329 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
364 AGTAGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 ---AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
402 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
437 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
*
472 AGTGAGT-AACTTAATTCAGGGTAATTAAG
1 AGT-AATCAACTTAATTCAGGGTAATTAAG
501 CAGCAGAGAT
Statistics
Matches: 132, Mismatches: 1, Indels: 5
0.96 0.01 0.04
Matches are distributed among these distances:
35 95 0.72
36 2 0.02
38 35 0.27
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (35 bp):
AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
Found at i:6082 original size:17 final size:17
Alignment explanation
Indices: 6060--6096 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6050 TCGCATAATT
*
6060 TCTTAACTGCATGCTCC
1 TCTTAACTGCACGCTCC
6077 TCTTAACTGCACGCTCC
1 TCTTAACTGCACGCTCC
6094 TCT
1 TCT
6097 GATTCTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.38, G:0.11, T:0.35
Consensus pattern (17 bp):
TCTTAACTGCACGCTCC
Found at i:7032 original size:11 final size:11
Alignment explanation
Indices: 6989--7026 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6979 TTCCTATATA
*
6989 AAATAAATTAT
1 AAATTAATTAT
7000 CAAA-TAATTAT
1 -AAATTAATTAT
7011 AAATTAATTAT
1 AAATTAATTAT
7022 AAATT
1 AAATT
7027 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:7416 original size:41 final size:42
Alignment explanation
Indices: 7344--7427 Score: 143
Period size: 41 Copynumber: 2.0 Consensus size: 42
7334 ACAAAATTTC
*
7344 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAAATTTTCTTAAAAGAATTTATAAAATAAA
*
7386 ATTTTTTAACT-AAATTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAAATTTTCTTAAAAGAATTTATAAAATAAA
7427 A
1 A
7428 CAGCCGCACG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 30 0.75
42 10 0.25
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (42 bp):
ATTTCTTAACTGAAATTTTCTTAAAAGAATTTATAAAATAAA
Found at i:10352 original size:20 final size:20
Alignment explanation
Indices: 10329--10367 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10319 ACAAGTTAAA
10329 TAAA-TACTTAATACAATTAC
1 TAAATTACTTAATA-AATTAC
*
10349 TAAATTGCTTAATAAATTA
1 TAAATTACTTAATAAATTA
10368 TAGATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (20 bp):
TAAATTACTTAATAAATTAC
Found at i:19883 original size:16 final size:15
Alignment explanation
Indices: 19850--19885 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
19840 AGACCTGAAT
*
19850 CCGAACCTGAAATGC
1 CCGAACCTGAAATAC
19865 CCGAACCTGAAAATAC
1 CCGAACCTG-AAATAC
19881 CCGAA
1 CCGAA
19886 TCCGAAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.39, C:0.33, G:0.17, T:0.11
Consensus pattern (15 bp):
CCGAACCTGAAATAC
Found at i:21684 original size:32 final size:32
Alignment explanation
Indices: 21643--21706 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
21633 AAGGGAGAAG
*
21643 AAAACGCTAGGCATC-CCCCTTTCTATTTCTTT
1 AAAACGCTAGCCATCTCCCC-TTCTATTTCTTT
21675 AAAACGCTAGCCATCTCCCCTTCTATTTCTTT
1 AAAACGCTAGCCATCTCCCCTTCTATTTCTTT
21707 TTTCCCTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.38
Consensus pattern (32 bp):
AAAACGCTAGCCATCTCCCCTTCTATTTCTTT
Found at i:24491 original size:39 final size:38
Alignment explanation
Indices: 24393--24511 Score: 123
Period size: 38 Copynumber: 3.0 Consensus size: 38
24383 TTATGATGAA
* *
24393 GAAGAAGCGGAAACAAGAAGAAGATGAAGAAAAGGATGAGAT
1 GAAGAAGCGG--ACAA-AA-AAGAAGAAGAAAAAGATGAGAT
** *
24435 GAAGAAGAAG-CGGAAAAAGAAGAAGAAAAAGATGAGAT
1 GAAGAAGCGGAC-AAAAAAGAAGAAGAAAAAGATGAGAT
*
24473 GAAGAAGCGGTACAAAAAAAAAGAAGAAAAAGATGAGAT
1 GAAGAAGCGG-ACAAAAAAGAAGAAGAAAAAGATGAGAT
24512 AATTGGGATT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
38 28 0.43
39 27 0.42
40 2 0.03
42 8 0.12
ACGTcount: A:0.59, C:0.04, G:0.30, T:0.07
Consensus pattern (38 bp):
GAAGAAGCGGACAAAAAAGAAGAAGAAAAAGATGAGAT
Found at i:24846 original size:11 final size:11
Alignment explanation
Indices: 24830--24864 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
24820 TTTTTCTGTT
24830 TTTTGTTTTTG
1 TTTTGTTTTTG
*
24841 TTTTGTTTTCG
1 TTTTGTTTTTG
24852 TTTTGTTTTTG
1 TTTTGTTTTTG
24863 TT
1 TT
24865 GCGCTGTTAA
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:26535 original size:17 final size:17
Alignment explanation
Indices: 26515--26565 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
26505 TAAATGAAAT
26515 TATTAGACATGTTAATG
1 TATTAGACATGTTAATG
26532 TATT----AT-TTAAAT-
1 TATTAGACATGTT-AATG
26544 TATTAGACATGTTAATG
1 TATTAGACATGTTAATG
26561 TATTA
1 TATTA
26566 TTTAAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 14
0.66 0.00 0.34
Matches are distributed among these distances:
12 6 0.22
13 5 0.19
16 5 0.19
17 11 0.41
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (17 bp):
TATTAGACATGTTAATG
Found at i:26543 original size:29 final size:29
Alignment explanation
Indices: 26511--26598 Score: 167
Period size: 29 Copynumber: 3.0 Consensus size: 29
26501 TAATTAAATG
26511 AAATTATTAGACATGTTAATGTATTATTT
1 AAATTATTAGACATGTTAATGTATTATTT
26540 AAATTATTAGACATGTTAATGTATTATTT
1 AAATTATTAGACATGTTAATGTATTATTT
*
26569 AAATTATTAGACATGTTAATGGATTATTT
1 AAATTATTAGACATGTTAATGTATTATTT
26598 A
1 A
26599 TTAAAAAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (29 bp):
AAATTATTAGACATGTTAATGTATTATTT
Found at i:27767 original size:13 final size:13
Alignment explanation
Indices: 27749--27776 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
27739 GAAAGAAGTT
27749 TTCTTTTTCATCA
1 TTCTTTTTCATCA
27762 TTCTTTTTCATCA
1 TTCTTTTTCATCA
27775 TT
1 TT
27777 TTAGATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (13 bp):
TTCTTTTTCATCA
Found at i:33442 original size:11 final size:11
Alignment explanation
Indices: 33426--33451 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33416 CATACCAGTT
33426 TAATTACATAA
1 TAATTACATAA
33437 TAATTACATAA
1 TAATTACATAA
33448 TAAT
1 TAAT
33452 AACAAGACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATTACATAA
Found at i:34862 original size:24 final size:24
Alignment explanation
Indices: 34830--34890 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
34820 AGAGAATGAG
34830 ACTTGATGAGTTGCCAAAA-TCGAA
1 ACTTGATGAGTTGCCAAAACT-GAA
*
34854 ACTTGATGA-TTCGCTAAAACTGAA
1 ACTTGATGAGTT-GCCAAAACTGAA
*
34878 ACTTGATGTGTTG
1 ACTTGATGAGTTG
34891 GATGATCGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.06
24 27 0.84
25 3 0.09
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (24 bp):
ACTTGATGAGTTGCCAAAACTGAA
Found at i:35153 original size:16 final size:17
Alignment explanation
Indices: 35114--35154 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
35104 GGAAGGTATC
35114 TTAT-TATTTATGATTA
1 TTATATATTTATGATTA
*
35130 TTATTATATTTAT-ATTT
1 TTA-TATATTTATGATTA
35147 TTATATAT
1 TTATATAT
35155 CACAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 7 0.32
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TTATATATTTATGATTA
Found at i:36936 original size:13 final size:13
Alignment explanation
Indices: 36918--36966 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
36908 TCTATTGAAA
36918 AAAAAAATCAAAG
1 AAAAAAATCAAAG
*
36931 AAAAAAATACAACAT
1 AAAAAAAT-CAA-AG
* *
36946 AAAAAAATTAGAG
1 AAAAAAATCAAAG
36959 AAAAAAAT
1 AAAAAAAT
36967 TGTAATTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 17 0.57
14 4 0.13
15 9 0.30
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAAAATCAAAG
Found at i:38281 original size:33 final size:33
Alignment explanation
Indices: 38242--38310 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
38232 TTGCAAGTCG
38242 AAAACAATACCAAAATCTGTTTTTGGGTAAGAA
1 AAAACAATACCAAAATCTGTTTTTGGGTAAGAA
38275 AAAACAATACCAAAATCTGTTTTTGGGTAAGAA
1 AAAACAATACCAAAATCTGTTTTTGGGTAAGAA
38308 AAA
1 AAA
38311 TACCCATTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (33 bp):
AAAACAATACCAAAATCTGTTTTTGGGTAAGAA
Found at i:40201 original size:23 final size:23
Alignment explanation
Indices: 40113--40201 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 23
40103 TTGGGTAGCG
* *
40113 CTCCGCGCAAGAGCTCGGGTGAGC
1 CTCCGCGCAAGAGC-AGGGTGAGT
* * *
40137 CTCCGTGCAAAAGCA-AGTGAGTT
1 CTCCGCGCAAGAGCAGGGTGAG-T
* **
40160 CTCCGCACAAGAGTTGGGTGAGT
1 CTCCGCGCAAGAGCAGGGTGAGT
*
40183 CTCCGTGCAAGAGCAGGGT
1 CTCCGCGCAAGAGCAGGGT
40202 AGTAATACAC
Statistics
Matches: 48, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
22 5 0.10
23 26 0.54
24 17 0.35
ACGTcount: A:0.22, C:0.26, G:0.34, T:0.18
Consensus pattern (23 bp):
CTCCGCGCAAGAGCAGGGTGAGT
Found at i:40435 original size:34 final size:34
Alignment explanation
Indices: 40396--40468 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
40386 TTAAATTGCA
* * *
40396 AAGGGGTGCGTAACGCCTTCCCCATTAGAATTGG
1 AAGGGGGGCGTAACGCCTCCCCCATTAAAATTGG
*
40430 AAGGGGGGCGTAAGGCCTCCCCCATTAAAATTGG
1 AAGGGGGGCGTAACGCCTCCCCCATTAAAATTGG
40464 AAGGG
1 AAGGG
40469 TTAAAAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.19
Consensus pattern (34 bp):
AAGGGGGGCGTAACGCCTCCCCCATTAAAATTGG
Found at i:40513 original size:50 final size:50
Alignment explanation
Indices: 40424--40518 Score: 147
Period size: 49 Copynumber: 1.9 Consensus size: 50
40414 TCCCCATTAG
*
40424 AATTGGAAGGGGGGCGTAAGGCCTCCCCCATTAAAATTGGAAGGGTTAAA
1 AATTGGAAGGGGGGCGTAACGCCTCCCCCATTAAAATTGGAAGGGTTAAA
* *
40474 AATTGG-AGGGGGGCGTAACGCCTCCCCCATATTACATTGGAAGGG
1 AATTGGAAGGGGGGCGTAACGCCTCCCCCAT-TAAAATTGGAAGGG
40519 GGGCTCGCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 23 0.56
50 18 0.44
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (50 bp):
AATTGGAAGGGGGGCGTAACGCCTCCCCCATTAAAATTGGAAGGGTTAAA
Found at i:40827 original size:26 final size:26
Alignment explanation
Indices: 40773--40834 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
40763 TTTTAATACT
* *
40773 CACACCA-GGGGTCGCCCTCCTTACT
1 CACACCAGGGGGTCGCCCTCCCTACA
40798 CACACCAGGGGGTCG-CCTCCCTAGCA
1 CACACCAGGGGGTCGCCCTCCCTA-CA
*
40824 CACAGCAGGGG
1 CACACCAGGGG
40835 TTGTACCCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.13
Consensus pattern (26 bp):
CACACCAGGGGGTCGCCCTCCCTACA
Found at i:40834 original size:25 final size:25
Alignment explanation
Indices: 40773--40835 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
40763 TTTTAATACT
* *
40773 CACACCAGGGGTCGCCCTCCTTACT
1 CACACCAGGGGTCGCCCTCCCTACA
40798 CACACCAGGGGGTCG-CCTCCCTAGCA
1 CACACCA-GGGGTCGCCCTCCCTA-CA
*
40824 CACAGCAGGGGT
1 CACACCAGGGGT
40836 TGTACCCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.14
Consensus pattern (25 bp):
CACACCAGGGGTCGCCCTCCCTACA
Found at i:41170 original size:29 final size:29
Alignment explanation
Indices: 41128--41185 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
41118 AAAAAAATAT
41128 GAGCACTTATCTTTGGAGCTTTAGGAGTG
1 GAGCACTTATCTTTGGAGCTTTAGGAGTG
41157 GAGCACTTATCTTTGGAGCTTTAGGAGTG
1 GAGCACTTATCTTTGGAGCTTTAGGAGTG
41186 AATTGCACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (29 bp):
GAGCACTTATCTTTGGAGCTTTAGGAGTG
Found at i:41827 original size:24 final size:24
Alignment explanation
Indices: 41797--41845 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
41787 CAACGGGGTT
41797 GCGCCATACCCACTCTTAGAGGGC
1 GCGCCATACCCACTCTTAGAGGGC
*
41821 GCGCCATACCCACTCTTAGGGGGC
1 GCGCCATACCCACTCTTAGAGGGC
41845 G
1 G
41846 TGCAATGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.37, G:0.29, T:0.16
Consensus pattern (24 bp):
GCGCCATACCCACTCTTAGAGGGC
Found at i:42173 original size:36 final size:36
Alignment explanation
Indices: 42125--42213 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 36
42115 TTATGTATTA
* *
42125 GGCGACTTAGGCCAGCGGCGTTATAGCCAAGCATTG
1 GGCGACTAAGGCCAGCGGCGTTATAGCAAAGCATTG
* *
42161 GGCGACTAAGGCCAGCGGTGTTATAGCAAAGTATTG
1 GGCGACTAAGGCCAGCGGCGTTATAGCAAAGCATTG
42197 GGCGACTAAGGCCAGCG
1 GGCGACTAAGGCCAGCG
42214 ACGCTACAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.25, C:0.22, G:0.35, T:0.18
Consensus pattern (36 bp):
GGCGACTAAGGCCAGCGGCGTTATAGCAAAGCATTG
Found at i:44235 original size:45 final size:45
Alignment explanation
Indices: 44171--44256 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
44161 TTCTTCAAAT
44171 AAGAACGTGGGTGGTTACCTCACTCTTGATGAAGTAACTGCTTTG
1 AAGAACGTGGGTGGTTACCTCACTCTTGATGAAGTAACTGCTTTG
*
44216 AAGAACGTGGGTGGTTACCTCATTCTTGATGAAGTAACTGC
1 AAGAACGTGGGTGGTTACCTCACTCTTGATGAAGTAACTGC
44257 CTATTGGCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (45 bp):
AAGAACGTGGGTGGTTACCTCACTCTTGATGAAGTAACTGCTTTG
Found at i:44320 original size:31 final size:31
Alignment explanation
Indices: 44280--44367 Score: 140
Period size: 31 Copynumber: 2.8 Consensus size: 31
44270 AATACTTGGT
* * *
44280 GAGTGTTTACGGTATACCTTTGGTTGGTATG
1 GAGTATTTACGGTATACCTTTGGTGGGTAGG
44311 GAGTATTTACGGTATACCTTTGGTGGGTAGG
1 GAGTATTTACGGTATACCTTTGGTGGGTAGG
44342 GAGTATTTACGGTATACCTTTTGGTG
1 GAGTATTTACGGTATACC-TTTGGTG
44368 AGTAATCATG
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 46 0.87
32 7 0.13
ACGTcount: A:0.18, C:0.10, G:0.32, T:0.40
Consensus pattern (31 bp):
GAGTATTTACGGTATACCTTTGGTGGGTAGG
Found at i:47283 original size:27 final size:26
Alignment explanation
Indices: 47253--47314 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
47243 AGAGGTAATT
*
47253 AGGGTGGGATTTTATTTTTTT-TTACAG
1 AGGGTGGG-TTTT-TTTTTTTCGTACAG
*
47280 AGGGTAGGTTTTTTTTTTTCGGTACAG
1 AGGGTGGGTTTTTTTTTTTC-GTACAG
47307 AGGGTGGG
1 AGGGTGGG
47315 GTTTATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 7 0.23
26 4 0.13
27 19 0.63
ACGTcount: A:0.16, C:0.05, G:0.34, T:0.45
Consensus pattern (26 bp):
AGGGTGGGTTTTTTTTTTTCGTACAG
Done.