Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002214.1 Kokia drynarioides strain JFW-HI SEQ_114205, 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: 66089
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:783 original size:6 final size:7
Alignment explanation
Indices: 760--794 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
750 GGGTGGCAAT
760 GAAGAGG
1 GAAGAGG
767 GAAGAGG
1 GAAGAGG
774 GAAG-GG
1 GAAGAGG
780 GAAG-GG
1 GAAGAGG
786 GAAGAGG
1 GAAGAGG
793 GA
1 GA
795 TTTTCCCGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (7 bp):
GAAGAGG
Found at i:5050 original size:24 final size:24
Alignment explanation
Indices: 5023--5072 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
5013 TCATTAATAA
* *
5023 ATAAACGAGTCAATAAACGAACTT
1 ATAAACAAGCCAATAAACGAACTT
* *
5047 ATAAATAAGCCAATAAACGAGCTT
1 ATAAACAAGCCAATAAACGAACTT
5071 AT
1 AT
5073 TCGTGAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (24 bp):
ATAAACAAGCCAATAAACGAACTT
Found at i:7983 original size:25 final size:21
Alignment explanation
Indices: 7955--8003 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 21
7945 AACCCAAAAC
7955 TATAAGAACAATAAATATTAATTGT
1 TATAA-AA-AATAAATA-TAATT-T
*
7980 TATAAAAAATATATATAATTT
1 TATAAAAAATAAATATAATTT
8001 TAT
1 TAT
8004 TTTAGTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 7 0.30
24 2 0.09
25 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (21 bp):
TATAAAAAATAAATATAATTT
Found at i:8820 original size:16 final size:16
Alignment explanation
Indices: 8799--8829 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8789 AATTTATTAA
8799 TAATGTTAAAAAAATC
1 TAATGTTAAAAAAATC
*
8815 TAATGTTATAAAAAT
1 TAATGTTAAAAAAAT
8830 AACATACACA
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:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
TAATGTTAAAAAAATC
Found at i:11108 original size:36 final size:36
Alignment explanation
Indices: 11001--11109 Score: 200
Period size: 36 Copynumber: 3.0 Consensus size: 36
10991 TTTGTTCTTA
*
11001 AATTTTCCAGTCATTAAGACTTGTTTTATGTATTGC
1 AATTTTCCAGTCATTAAGACTTGTTTTATGTATTGT
11037 AATTTTCCAGTCATTAAGACTTGTTTTATGTATTGT
1 AATTTTCCAGTCATTAAGACTTGTTTTATGTATTGT
*
11073 AATTTTCCAGTCATTAAGACTTTTTTTATGTATTGT
1 AATTTTCCAGTCATTAAGACTTGTTTTATGTATTGT
11109 A
1 A
11110 TCTTTAATGG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.50
Consensus pattern (36 bp):
AATTTTCCAGTCATTAAGACTTGTTTTATGTATTGT
Found at i:17275 original size:93 final size:94
Alignment explanation
Indices: 17115--17285 Score: 218
Period size: 93 Copynumber: 1.8 Consensus size: 94
17105 ATAAACTCAG
* * * * *
17115 AACAAAGTTTGGGTAGAGATCGACAATTTTTCGAATACTAAAAATACTATCCGTTGCAAATGTGG
1 AACAAAGTTTGGGTAGAGATCGACAATTTTTCAAACACTAAAAATACTATCCGCTGCAAACGCGG
17180 ATTTAACCCCTCGAATAATGGATAGTAAA
66 ATTTAACCCCTCGAATAATGGATAGTAAA
* * * * ***
17209 AACAAAGTTTGGGTAGAGAT-GGCAATTTTTCAAACAGTAAAAATATTATCTGCTGTGGACGCGG
1 AACAAAGTTTGGGTAGAGATCGACAATTTTTCAAACACTAAAAATACTATCCGCTGCAAACGCGG
*
17273 ATTTAACCTCTCG
66 ATTTAACCCCTCG
17286 GATATCTATT
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
93 44 0.69
94 20 0.31
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (94 bp):
AACAAAGTTTGGGTAGAGATCGACAATTTTTCAAACACTAAAAATACTATCCGCTGCAAACGCGG
ATTTAACCCCTCGAATAATGGATAGTAAA
Found at i:18760 original size:24 final size:24
Alignment explanation
Indices: 18728--18773 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
18718 TCATTTAACT
* *
18728 TAATCGAACGTGTTCATGAACATA
1 TAATCGAACATGTTCACGAACATA
*
18752 TAATTGAACATGTTCACGAACA
1 TAATCGAACATGTTCACGAACA
18774 ATGCTAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (24 bp):
TAATCGAACATGTTCACGAACATA
Found at i:24062 original size:16 final size:16
Alignment explanation
Indices: 24025--24065 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
24015 TTAGGGTTTA
* *
24025 AAATTTTTAATTAATT
1 AAATATTTATTTAATT
24041 -AA-ATTTATTTAATT
1 AAATATTTATTTAATT
24055 AAATATTTATT
1 AAATATTTATT
24066 CTCATTCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.48
15 4 0.19
16 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATATTTATTTAATT
Found at i:25260 original size:4 final size:4
Alignment explanation
Indices: 25251--25325 Score: 80
Period size: 4 Copynumber: 18.0 Consensus size: 4
25241 AACGGTTATT
*
25251 GAAA GAAA GAAA GAAA GACAA GAAA GAAA GAAA G-AA GGAA GAAA GAGAA
1 GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA
* *
25300 GAAA AAAA GGAAGA GAAT GAAA GAAA
1 GAAA GAAA -GAA-A GAAA GAAA GAAA
25326 TGTAATATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
3 3 0.05
4 44 0.72
5 13 0.21
6 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.28, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:25275 original size:17 final size:17
Alignment explanation
Indices: 25253--25285 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
25243 CGGTTATTGA
25253 AAGAAAGAAAGAAAGAC
1 AAGAAAGAAAGAAAGAC
25270 AAGAAAGAAAGAAAGA
1 AAGAAAGAAAGAAAGA
25286 AGGAAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAAGAAAGAC
Found at i:25277 original size:21 final size:20
Alignment explanation
Indices: 25251--25325 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
25241 AACGGTTATT
25251 GAAAGAAAGAAAGAAAGACAA
1 GAAAGAAAGAAAGAAAGA-AA
*
25272 GAAAGAAAGAAAG-AAGGAA
1 GAAAGAAAGAAAGAAAGAAA
*
25291 GAAAGAGAAGAAAAAAAGGAAGA
1 GAAAGA-AAGAAAGAAA-GAA-A
*
25314 GAATGAAAGAAA
1 GAAAGAAAGAAA
25326 TGTAATATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 8 0.17
20 9 0.20
21 15 0.33
22 8 0.17
23 6 0.13
ACGTcount: A:0.69, C:0.01, G:0.28, T:0.01
Consensus pattern (20 bp):
GAAAGAAAGAAAGAAAGAAA
Found at i:25865 original size:22 final size:21
Alignment explanation
Indices: 25835--25876 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
25825 AAATAGTTAT
*
25835 ATAATAAATTTAGAAAGAATTA
1 ATAAAAAATTTA-AAAGAATTA
*
25857 ATAAAAAATTTAAAATAATT
1 ATAAAAAATTTAAAAGAATT
25877 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
ATAAAAAATTTAAAAGAATTA
Found at i:27292 original size:43 final size:43
Alignment explanation
Indices: 27210--27294 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
27200 ATTAACATGT
* *
27210 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
27253 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
27295 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:27761 original size:6 final size:6
Alignment explanation
Indices: 27750--27797 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
27740 TAGCTCCTGC
** * * *
27750 CCAGAG CCAGAG ATAGAG CCAGAG CCAGAG CAAGAG CAAGAG CAAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
27798 GAAGAGGAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.42, C:0.23, G:0.33, T:0.02
Consensus pattern (6 bp):
CCAGAG
Found at i:27773 original size:18 final size:18
Alignment explanation
Indices: 27750--27803 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
27740 TAGCTCCTGC
27750 CCAGAGCCAGAG-ATAGAG
1 CCAGAGCCAGAGCA-AGAG
27768 CCAGAGCCAGAGCAAGAG
1 CCAGAGCCAGAGCAAGAG
* * *
27786 CAAGAGCAAGAGGAAGAG
1 CCAGAGCCAGAGCAAGAG
27804 GAAGAGGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 31 0.97
19 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.35, T:0.02
Consensus pattern (18 bp):
CCAGAGCCAGAGCAAGAG
Found at i:27779 original size:12 final size:12
Alignment explanation
Indices: 27752--27803 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
27742 GCTCCTGCCC
27752 AGAGCCAGAG-A
1 AGAGCCAGAGCA
*
27763 TAGAGCCAGAGCC
1 -AGAGCCAGAGCA
*
27776 AGAGCAAGAGCA
1 AGAGCCAGAGCA
* *
27788 AGAGCAAGAGGA
1 AGAGCCAGAGCA
27800 AGAG
1 AGAG
27804 GAAGAGGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.44, C:0.17, G:0.37, T:0.02
Consensus pattern (12 bp):
AGAGCCAGAGCA
Found at i:27802 original size:6 final size:6
Alignment explanation
Indices: 27776--27816 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
27766 AGCCAGAGCC
* * *
27776 AGAGCA AGAGCA AGAGCA AGAGGA AGAGGA AGAGGA AGAGG
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGG
27817 CATTGTATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.49, C:0.07, G:0.44, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:27808 original size:18 final size:18
Alignment explanation
Indices: 27764--27816 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
27754 AGCCAGAGAT
* * *
27764 AGAGCCAGAGCCAGAGCA
1 AGAGCAAGAGCAAGAGGA
27782 AGAGCAAGAGCAAGAGGA
1 AGAGCAAGAGCAAGAGGA
* *
27800 AGAGGAAGAGGAAGAGG
1 AGAGCAAGAGCAAGAGG
27817 CATTGTATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.45, C:0.13, G:0.42, T:0.00
Consensus pattern (18 bp):
AGAGCAAGAGCAAGAGGA
Found at i:27816 original size:12 final size:12
Alignment explanation
Indices: 27776--27815 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
27766 AGCCAGAGCC
*
27776 AGAGCAAGAGCA
1 AGAGCAAGAGGA
27788 AGAGCAAGAGGA
1 AGAGCAAGAGGA
*
27800 AGAGGAAGAGGA
1 AGAGCAAGAGGA
27812 AGAG
1 AGAG
27816 GCATTGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.50, C:0.07, G:0.42, T:0.00
Consensus pattern (12 bp):
AGAGCAAGAGGA
Found at i:28204 original size:14 final size:15
Alignment explanation
Indices: 28180--28209 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28170 TAAATTTCAT
28180 ACCTATAAACCCTAA
1 ACCTATAAACCCTAA
28195 ACCT-TAAACCCTAA
1 ACCTATAAACCCTAA
28209 A
1 A
28210 TTAGAAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (15 bp):
ACCTATAAACCCTAA
Found at i:30648 original size:24 final size:24
Alignment explanation
Indices: 30621--30668 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
30611 CCACCATACA
30621 TGGAGTTGGATCTTCATTTTCTAC
1 TGGAGTTGGATCTTCATTTTCTAC
30645 TGGAGTTGGATCTTCATTTTCTAC
1 TGGAGTTGGATCTTCATTTTCTAC
30669 AAGTTCCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (24 bp):
TGGAGTTGGATCTTCATTTTCTAC
Found at i:31520 original size:35 final size:35
Alignment explanation
Indices: 31473--31544 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
31463 TATTTTTATT
*
31473 AAATTAATAATTTTT-AATAATACTTTAGTCAAATA
1 AAATAAATAATTTTTGAATAATACTTTAGT-AAATA
* * *
31508 AAATAAATAATTTTTGTATATTATTTTAGTAAATA
1 AAATAAATAATTTTTGAATAATACTTTAGTAAATA
31543 AA
1 AA
31545 TATTTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 21 0.66
36 11 0.34
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (35 bp):
AAATAAATAATTTTTGAATAATACTTTAGTAAATA
Found at i:33177 original size:31 final size:31
Alignment explanation
Indices: 33139--33197 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
33129 CGTTAAATTG
*
33139 AATAATTCAATAAGTTAAATAAAAACTTTTA
1 AATAATTCAATAACTTAAATAAAAACTTTTA
* *
33170 AATAATTCAATGACTTAAATGAAAACTT
1 AATAATTCAATAACTTAAATAAAAACTT
33198 ATCCATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (31 bp):
AATAATTCAATAACTTAAATAAAAACTTTTA
Found at i:36504 original size:30 final size:28
Alignment explanation
Indices: 36468--36535 Score: 102
Period size: 27 Copynumber: 2.4 Consensus size: 28
36458 CAAATGATTT
36468 TAAAATTATTAAAATTATTTTTTTGAAATA
1 TAAAATTATTAAAATTATTTTTTT--AATA
*
36498 TAAAATTATT-ATATTATTTTTTTAATA
1 TAAAATTATTAAAATTATTTTTTTAATA
36525 TAAAATTATTA
1 TAAAATTATTA
36536 TACGACTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 14 0.39
29 12 0.33
30 10 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTTTAATA
Found at i:37639 original size:21 final size:21
Alignment explanation
Indices: 37615--37693 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
37605 AATCATATAG
*
37615 TAATTTTATATTTTTAAAAAA
1 TAATTTTATAATTTTAAAAAA
* *
37636 TAATATAATAATTTT----AA
1 TAATTTTATAATTTTAAAAAA
*
37653 TAATTTTAT-ATTTCAAAAAAA
1 TAATTTTATAATTT-TAAAAAA
37674 TAATTTTAATAATTTTAAAA
1 TAATTTT-ATAATTTTAAAA
37694 TCATTTGCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
16 4 0.09
17 9 0.20
21 21 0.48
22 6 0.14
23 4 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTTTATAATTTTAAAAAA
Found at i:37641 original size:29 final size:30
Alignment explanation
Indices: 37603--37693 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 30
37593 ATTGGAAATT
* * *
37603 AAAATCATATAGTAATTTT-ATATTTTTAA
1 AAAATAATATAATAATTTTAATAATTTTAA
37632 AAAATAATATAATAATTTTAATAATTTT-A
1 AAAATAATATAATAATTTTAATAATTTTAA
* ** * *
37661 TATTTCAAAAAAATAATTTTAATAATTTTAA
1 AAAAT-AATATAATAATTTTAATAATTTTAA
37692 AA
1 AA
37694 TCATTTGCTA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
29 20 0.40
30 28 0.56
31 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (30 bp):
AAAATAATATAATAATTTTAATAATTTTAA
Found at i:37657 original size:38 final size:39
Alignment explanation
Indices: 37615--37691 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
37605 AATCATATAG
**
37615 TAATTTTATATTTTTAAAAAATAA-TATAATAATTTTAA
1 TAATTTTATATTTCAAAAAAATAATTATAATAATTTTAA
*
37653 TAATTTTATATTTCAAAAAAATAATTTTAATAATTTTAA
1 TAATTTTATATTTCAAAAAAATAATTATAATAATTTTAA
37692 AATCATTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 22 0.63
39 13 0.37
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (39 bp):
TAATTTTATATTTCAAAAAAATAATTATAATAATTTTAA
Found at i:42153 original size:6 final size:6
Alignment explanation
Indices: 42142--42172 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42132 ACATCATACT
42142 GCACAA GCACAA GCACAA GCACAA GCACAA G
1 GCACAA GCACAA GCACAA GCACAA GCACAA G
42173 GTTCATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.32, G:0.19, T:0.00
Consensus pattern (6 bp):
GCACAA
Found at i:45809 original size:17 final size:18
Alignment explanation
Indices: 45776--45810 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45766 TTCCGATGTT
45776 AGAAAAAAAGCGTTGAAAG
1 AGAAAAAAAGCG-TGAAAG
45795 AGAAAAAAAGC-TGAAA
1 AGAAAAAAAGCGTGAAA
45811 AAAACAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
19 11 0.69
ACGTcount: A:0.63, C:0.06, G:0.23, T:0.09
Consensus pattern (18 bp):
AGAAAAAAAGCGTGAAAG
Found at i:52928 original size:22 final size:21
Alignment explanation
Indices: 52878--52930 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
52868 TGCAACGGAG
52878 AGAAAGGAAACAAAATCAAAGA
1 AGAAA-GAAACAAAATCAAAGA
*
52900 A-AGAAGAAACAAAATATAAAGA
1 AGA-AAGAAACAAAAT-CAAAGA
52922 AGAAAGAAA
1 AGAAAGAAA
52931 TAAGAGGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 11 0.41
22 15 0.56
23 1 0.04
ACGTcount: A:0.72, C:0.06, G:0.17, T:0.06
Consensus pattern (21 bp):
AGAAAGAAACAAAATCAAAGA
Found at i:53514 original size:29 final size:30
Alignment explanation
Indices: 53457--53517 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
53447 TGGATTCGAG
*
53457 TGATTGATTTGTCATTTTTATAAAATTTAA
1 TGATTGAGTTGTCATTTTTATAAAATTTAA
53487 TGATTGAGTTGTCATTTTT-TAAAATTTAA
1 TGATTGAGTTGTCATTTTTATAAAATTTAA
53516 TG
1 TG
53518 GTTATTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.52
Consensus pattern (30 bp):
TGATTGAGTTGTCATTTTTATAAAATTTAA
Found at i:54101 original size:17 final size:17
Alignment explanation
Indices: 54074--54106 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54064 TTATATGAAG
54074 TTTATATATAAGATATAT
1 TTTATATATAA-ATATAT
54092 TTTA-ATATAAATATA
1 TTTATATATAAATATA
54107 AAATACAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTATATATAAATATAT
Found at i:54181 original size:10 final size:10
Alignment explanation
Indices: 54166--54190 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54156 CATATTGTAT
54166 AAAATATAAA
1 AAAATATAAA
54176 AAAATATAAA
1 AAAATATAAA
54186 AAAAT
1 AAAAT
54191 CAAATGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAATATAAA
Done.