Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020035.1 Corchorus olitorius cultivar O-4 contig20068, 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: 38652
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7171 original size:30 final size:30
Alignment explanation
Indices: 7137--7193 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
7127 CATATACGGA
7137 CCATACCTCAAAGTA-AAAGAAAGGAATATT
1 CCATACCTCAAAG-AGAAAGAAAGGAATATT
7167 CCATACCTCAAAGAGAAAGAAAGGAAT
1 CCATACCTCAAAGAGAAAGAAAGGAAT
7194 CCAAATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.16
Consensus pattern (30 bp):
CCATACCTCAAAGAGAAAGAAAGGAATATT
Found at i:7386 original size:1 final size:1
Alignment explanation
Indices: 7380--7404 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
7370 GCAAATTGTA
7380 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
7405 GTGTGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8255 original size:2 final size:2
Alignment explanation
Indices: 8248--8275 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8238 TTGAATCTAG
8248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8276 CAATTGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10561 original size:42 final size:43
Alignment explanation
Indices: 10510--10603 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
10500 AGTGCATTAC
* *
10510 CTAA-ATTCTA-CTACATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAA
* *
10551 CTATTATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTACATCTCTAGATAATTCATCAAAATAAAA
10596 CTAATATT
1 CTAATATT
10604 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.14
45 35 0.80
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAA
Found at i:12031 original size:14 final size:14
Alignment explanation
Indices: 12012--12038 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12002 ATACAACACA
12012 CATATCAGATGAAC
1 CATATCAGATGAAC
12026 CATATCAGATGAA
1 CATATCAGATGAA
12039 GTGGTAAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (14 bp):
CATATCAGATGAAC
Found at i:16148 original size:14 final size:14
Alignment explanation
Indices: 16129--16155 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16119 ATACAACACA
16129 CATATCAGATGAAC
1 CATATCAGATGAAC
16143 CATATCAGATGAA
1 CATATCAGATGAA
16156 GTGGTAAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (14 bp):
CATATCAGATGAAC
Found at i:17322 original size:2 final size:2
Alignment explanation
Indices: 17315--17340 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17305 TTTCCATAAG
17315 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
17341 GGTAATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17508 original size:22 final size:21
Alignment explanation
Indices: 17456--17511 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
17446 TTAACCATTC
17456 ATTCAATTTTATT--AAGGCT
1 ATTCAATTTTATTAAAAGGCT
*
17475 ATT-AAGTCTTATTAAAAGGCTT
1 ATTCAA-TTTTATTAAAAGGC-T
17497 ATTCAATTTTATTAA
1 ATTCAATTTTATTAA
17512 GGCTCATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.07
19 9 0.30
21 5 0.17
22 12 0.40
23 2 0.07
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (21 bp):
ATTCAATTTTATTAAAAGGCT
Found at i:17528 original size:20 final size:20
Alignment explanation
Indices: 17464--17537 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
17454 TCATTCAATT
17464 TTATTAAGGCT-ATTAAGTC
1 TTATTAAGGCTCATTAAGTC
* *
17483 TTATTAAAAGGCTTATTCAA-TT
1 TTATT--AAGGCTCATT-AAGTC
17505 TTATTAAGGCTCATTAAGTC
1 TTATTAAGGCTCATTAAGTC
17525 TTA-TACAGGCTCA
1 TTATTA-AGGCTCA
17538 ATCCTTCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 9 0.20
20 20 0.43
21 6 0.13
22 9 0.20
23 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
TTATTAAGGCTCATTAAGTC
Found at i:17598 original size:10 final size:10
Alignment explanation
Indices: 17573--17644 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
17563 GCAATCAATT
17573 TTATTAAGGC
1 TTATTAAGGC
*
17583 -TATTAAGTC
1 TTATTAAGGC
17592 TTATTAAAAGGC
1 TTATT--AAGGC
**
17604 TTATTCAA-TT
1 TTATT-AAGGC
17614 TTATTAAGGC
1 TTATTAAGGC
*
17624 TTATTAAGTC
1 TTATTAAGGC
*
17634 TTATTTAGGC
1 TTATTAAGGC
17644 T
1 T
17645 CAATCCTTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
9 10 0.21
10 27 0.56
11 2 0.04
12 9 0.19
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.46
Consensus pattern (10 bp):
TTATTAAGGC
Found at i:17624 original size:20 final size:20
Alignment explanation
Indices: 17567--17729 Score: 91
Period size: 20 Copynumber: 8.0 Consensus size: 20
17557 AACCATGCAA
17567 TCAATTTTATTAAGGC-TAT
1 TCAATTTTATTAAGGCTTAT
*
17586 T-AAGTCTTATTAAAAGGCTTAT
1 TCAA-TTTTATT--AAGGCTTAT
17608 TCAATTTTATTAAGGCTTAT
1 TCAATTTTATTAAGGCTTAT
* * * *
17628 T-AAGTCTTATTTAGGCTCAA
1 TCAA-TTTTATTAAGGCTTAT
* * ***
17648 TC-CTTTTTTTCAAGAAATAT
1 TCAATTTTATT-AAGGCTTAT
* * * *
17668 TTAGTATTATGAAGGCTTAT
1 TCAATTTTATTAAGGCTTAT
* *
17688 TAAATCTTATTAAAAGGCTTAT
1 TCAATTTTATT--AAGGCTTAT
17710 TCAATTTTATTAAGGCTTAT
1 TCAATTTTATTAAGGCTTAT
17730 CAAGTCTTAT
Statistics
Matches: 104, Mismatches: 29, Indels: 21
0.68 0.19 0.14
Matches are distributed among these distances:
18 2 0.02
19 14 0.13
20 49 0.47
21 9 0.09
22 28 0.27
23 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
TCAATTTTATTAAGGCTTAT
Found at i:17644 original size:109 final size:107
Alignment explanation
Indices: 17439--17741 Score: 402
Period size: 109 Copynumber: 2.8 Consensus size: 107
17429 AAGCTATGTC
17439 TCAAGTCTTAACCATTCATTCAATTTTATTAAGGCTATTAAGTCTTATTAAAAGGCTTATTCAAT
1 TCAAGTC-TAACCA-TCATTCAATTTTATTAAGGCTATTAAGTCTTATTAAAAGGCTTATTCAAT
* **
17504 TTTATTAAGGCTCATTAAGTCTTATACAGGCTCAATCCTTCTTA
64 TTTATTAAGGCTTATTAAGTCTTATTTAGGCTCAATCCTTCTTA
* *
17548 TCAGGTCTCAACCATGCAATCAATTTTATTAAGGCTATTAAGTCTTATTAAAAGGCTTATTCAAT
1 TCAAGTCT-AACCAT-CATTCAATTTTATTAAGGCTATTAAGTCTTATTAAAAGGCTTATTCAAT
* *
17613 TTTATTAAGGCTTATTAAGTCTTATTTAGGCTCAATCCTTTTTT
64 TTTATTAAGGCTTATTAAGTCTTATTTAGGCTCAATCCTTCTTA
* * * * *
17657 TCAAG---AA--AT-ATTTAGTATTATGAAGGCTTATTAAATCTTATTAAAAGGCTTATTCAATT
1 TCAAGTCTAACCATCATTCAATTTTATTAAGGC-TATTAAGTCTTATTAAAAGGCTTATTCAATT
*
17716 TTATTAAGGCTTATCAAGTCTTATTT
65 TTATTAAGGCTTATTAAGTCTTATTT
17742 CATCAAATTA
Statistics
Matches: 176, Mismatches: 15, Indels: 13
0.86 0.07 0.06
Matches are distributed among these distances:
101 13 0.07
102 55 0.31
103 2 0.01
105 2 0.01
108 2 0.01
109 102 0.58
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (107 bp):
TCAAGTCTAACCATCATTCAATTTTATTAAGGCTATTAAGTCTTATTAAAAGGCTTATTCAATTT
TATTAAGGCTTATTAAGTCTTATTTAGGCTCAATCCTTCTTA
Found at i:17707 original size:22 final size:20
Alignment explanation
Indices: 17674--17740 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
17664 ATATTTAGTA
*
17674 TTATGAAGGCTTATTAAATC
1 TTATTAAGGCTTATTAAATC
* *
17694 TTATTAAAAGGCTTATTCAATT
1 TTATT--AAGGCTTATTAAATC
* *
17716 TTATTAAGGCTTATCAAGTC
1 TTATTAAGGCTTATTAAATC
17736 TTATT
1 TTATT
17741 TCATCAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 20 0.53
22 18 0.47
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
TTATTAAGGCTTATTAAATC
Found at i:18105 original size:25 final size:25
Alignment explanation
Indices: 18076--18127 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
18066 TATATCCTTT
*
18076 TAAGT-ACTCCCTCTGTTCCTTATTA
1 TAAGTCACACCCT-TGTTCCTTATTA
*
18101 TAAGTCCACACCCTTGTTCCTTTTTA
1 TAAGT-CACACCCTTGTTCCTTATTA
18127 T
1 T
18128 TTGTCTTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 5 0.22
26 12 0.52
27 6 0.26
ACGTcount: A:0.19, C:0.29, G:0.08, T:0.44
Consensus pattern (25 bp):
TAAGTCACACCCTTGTTCCTTATTA
Found at i:18402 original size:13 final size:15
Alignment explanation
Indices: 18367--18396 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18357 AACCGTTTTC
18367 CTTGGTTAAAGATTT
1 CTTGGTTAAAGATTT
18382 CTTGGTTAAAGATTT
1 CTTGGTTAAAGATTT
18397 TGGTTATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
CTTGGTTAAAGATTT
Found at i:18983 original size:31 final size:32
Alignment explanation
Indices: 18939--18998 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
18929 ATCAAACAAA
*
18939 ACCAGCAAAGAAAACAAC-CTAAAAAAAACCC
1 ACCAGCAAAGAAAACAACAATAAAAAAAACCC
** *
18970 ACCAGCAGTGAAAACCACAATAAAAAAAA
1 ACCAGCAAAGAAAACAACAATAAAAAAAA
18999 TTGAAAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 15 0.62
32 9 0.38
ACGTcount: A:0.62, C:0.25, G:0.08, T:0.05
Consensus pattern (32 bp):
ACCAGCAAAGAAAACAACAATAAAAAAAACCC
Found at i:20139 original size:126 final size:120
Alignment explanation
Indices: 19920--20164 Score: 400
Period size: 126 Copynumber: 2.0 Consensus size: 120
19910 ATTGATGATT
19920 TTATATATCACTTCTTCCACAAAATAACTTATATATTACATAAACATATGTTATACTCCATCCAT
1 TTATATATCACTTCTTCCACAAAATAACTTATATATTACATAAACATATGTTATACTCCATCCAT
*
19985 CCCTTTTTATCTGTCGGCAATAATCGAATTGTACATACGAAGGAATTTAGTTAAC
66 CCCTTTTTATCTGTCGACAATAATCGAATTGTACATACGAAGGAATTTAGTTAAC
*
20040 TTATATATTACTTCTTCCACAAAATAACTTATATATATATATTACATAAACATATGTTATACTCC
1 TTATATATCACTTCTTCCACAAAATAAC-----T-TATATATTACATAAACATATGTTATACTCC
* *
20105 ATCCATCCCTTTTTATCTGTCGACAATAATCGAATTGTATATATGAAGGAATTTAGTTAA
60 ATCCATCCCTTTTTATCTGTCGACAATAATCGAATTGTACATACGAAGGAATTTAGTTAA
20165 ATTCGTTAAA
Statistics
Matches: 115, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
120 27 0.23
125 1 0.01
126 87 0.76
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (120 bp):
TTATATATCACTTCTTCCACAAAATAACTTATATATTACATAAACATATGTTATACTCCATCCAT
CCCTTTTTATCTGTCGACAATAATCGAATTGTACATACGAAGGAATTTAGTTAAC
Found at i:21045 original size:90 final size:91
Alignment explanation
Indices: 20848--21086 Score: 354
Period size: 90 Copynumber: 2.6 Consensus size: 91
20838 AATAAGAAGA
* * * *
20848 TCAAATGTATCTATATCGTGTTTAAATTGATTAAATCCAAAATTGTTCAACTAAATGATTTTTTT
1 TCAAATGTGTCCATTTCATGTTTAAATTGATTAAATCCAAAATTGTTCAACT--A--ATTTTTTT
*
20913 TTAAAAGAAGATCAAACCTCTTAGAATTTG
62 TTAAAAGAAGATCAAACCTCTTAGAAATTG
*
20943 CCAAATGTGTCCATTTCATGTTTAAATTGATTAAATCCAAAATTGTTCAACTAA-TTTTTTTTAA
1 TCAAATGTGTCCATTTCATGTTTAAATTGATTAAATCCAAAATTGTTCAACTAATTTTTTTTTAA
*
21007 AAGAAGATCATACCTCTTAGAAATTG
66 AAGAAGATCAAACCTCTTAGAAATTG
* *
21033 TCAAATGTGTCCATTTCATGTTTAAATTGATTAAATCCAATATTATTCAACTAA
1 TCAAATGTGTCCATTTCATGTTTAAATTGATTAAATCCAAAATTGTTCAACTAA
21087 ATGATTTTTT
Statistics
Matches: 134, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
90 85 0.63
91 1 0.01
93 1 0.01
95 47 0.35
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (91 bp):
TCAAATGTGTCCATTTCATGTTTAAATTGATTAAATCCAAAATTGTTCAACTAATTTTTTTTTAA
AAGAAGATCAAACCTCTTAGAAATTG
Found at i:21656 original size:32 final size:32
Alignment explanation
Indices: 21615--21680 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
21605 AGATGAGGAG
21615 ATCAAATAATTAAATTGAAAATTATAAAAAAA
1 ATCAAATAATTAAATTGAAAATTATAAAAAAA
*
21647 ATCAAATAATTAAATTGAAAATTATTAAAAAA
1 ATCAAATAATTAAATTGAAAATTATAAAAAAA
21679 AT
1 AT
21681 GTAGGCTGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (32 bp):
ATCAAATAATTAAATTGAAAATTATAAAAAAA
Found at i:21791 original size:52 final size:52
Alignment explanation
Indices: 21713--21817 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
21703 ACGCACACTT
21713 ATCTACTAAATGAGGAGATCAAATAATTAAATTAAATTGTAAATTATTTAAA
1 ATCTACTAAATGAGGAGATCAAATAATTAAATTAAATTGTAAATTATTTAAA
21765 ATCTACTAAATGAGGAGATCAAATAATTAAATTAAATTGTAAATTATTTAAA
1 ATCTACTAAATGAGGAGATCAAATAATTAAATTAAATTGTAAATTATTTAAA
21817 A
1 A
21818 AAATATGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (52 bp):
ATCTACTAAATGAGGAGATCAAATAATTAAATTAAATTGTAAATTATTTAAA
Found at i:29793 original size:26 final size:24
Alignment explanation
Indices: 29764--29834 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 24
29754 AAGCGAACAC
*
29764 AAACACAAGGTAACAAACGAAGTCAT
1 AAACACAA-GTAACAAACAAAGTC-T
29790 AAACACTAAGTAACAAACAAAGTCT
1 AAACAC-AAGTAACAAACAAAGTCT
29815 -AACACAAAGTAA-AAACAAAG
1 AAACAC-AAGTAACAAACAAAG
29835 ATAATCATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 8 0.19
24 11 0.26
25 1 0.02
26 20 0.48
27 2 0.05
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.11
Consensus pattern (24 bp):
AAACACAAGTAACAAACAAAGTCT
Found at i:30246 original size:16 final size:16
Alignment explanation
Indices: 30222--30252 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30212 ACAACTCGTA
30222 TTAGCATTGAAAAATG
1 TTAGCATTGAAAAATG
*
30238 TTAGGATTGAAAAAT
1 TTAGCATTGAAAAAT
30253 CACAGATTGA
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:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (16 bp):
TTAGCATTGAAAAATG
Found at i:32030 original size:33 final size:35
Alignment explanation
Indices: 31961--32035 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
31951 AAAGGCTGTT
*
31961 GGGCCAGTGGCCCAGCGCCTAGACCACAGGCGCGC
1 GGGCCAGTGGCCCAGCACCTAGACCACAGGCGCGC
* *
31996 GGGCCAGTGGCCCAGCACCTAG-GC-TAGGCGCGC
1 GGGCCAGTGGCCCAGCACCTAGACCACAGGCGCGC
32029 GGGCCAG
1 GGGCCAG
32036 CGCCTTGGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 15 0.41
34 1 0.03
35 21 0.57
ACGTcount: A:0.16, C:0.37, G:0.40, T:0.07
Consensus pattern (35 bp):
GGGCCAGTGGCCCAGCACCTAGACCACAGGCGCGC
Found at i:32688 original size:27 final size:28
Alignment explanation
Indices: 32620--32688 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
32610 TTAAAATGTC
* *
32620 AAAATTACTGTTTTACCCTTGGTCAGCT
1 AAAATTACAGTTTTACCCCTGGTCAGCT
*
32648 AAAATTACCA-TTTTACCCCTGGT-TGACT
1 AAAATTA-CAGTTTTACCCCTGGTCAG-CT
32676 -AAATTACAGTTTT
1 AAAATTACAGTTTT
32689 GCCCTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 2 0.06
27 11 0.31
28 21 0.60
29 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (28 bp):
AAAATTACAGTTTTACCCCTGGTCAGCT
Found at i:35442 original size:21 final size:21
Alignment explanation
Indices: 35417--35499 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
35407 TATCTTAGAT
35417 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
35438 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
35459 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
35481 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
35500 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:35450 original size:25 final size:25
Alignment explanation
Indices: 35419--35467 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
35409 TCTTAGATAT
*
35419 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
35444 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
35468 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Done.