Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001485.1 Kokia drynarioides strain JFW-HI SEQ_113021, 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: 40329
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 218 characters in sequence are not A, C, G, or T
Found at i:233 original size:25 final size:25
Alignment explanation
Indices: 205--336 Score: 125
Period size: 23 Copynumber: 5.5 Consensus size: 25
195 AGCACGTCTC
*
205 GTGCTCTCTGTTATTAGCACTATGT
1 GTGCTCTCTGTTATTAGCACTTTGT
*
230 GTGCTCTCTG--ACTAGCACTTTGT
1 GTGCTCTCTGTTATTAGCACTTTGT
*
253 GTGCTCTCTG--ATTAGTACTTTGT
1 GTGCTCTCTGTTATTAGCACTTTGT
* * *
276 GTACTCTCT-AT-TTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTTTGT
** *
299 GTGCTCTCTGTTACCCAGCAC-TTAT
1 GTGCTCTCTGTTA-TTAGCACTTTGT
324 GTGCTCTCTGTTA
1 GTGCTCTCTGTTA
337 GTATTTTGGT
Statistics
Matches: 89, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
23 58 0.65
24 1 0.01
25 25 0.28
26 5 0.06
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (25 bp):
GTGCTCTCTGTTATTAGCACTTTGT
Found at i:236 original size:23 final size:23
Alignment explanation
Indices: 205--308 Score: 129
Period size: 23 Copynumber: 4.4 Consensus size: 23
195 AGCACGTCTC
*
205 GTGCTCTCTGTTATTAGCACTATGT
1 GTGCTCTCTG--ATTAGCACTTTGT
*
230 GTGCTCTCTGACTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
253 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
276 GTACTCTCT-ATTTAGCACTGTGT
1 GTGCTCTCTGA-TTAGCACTTTGT
299 GTGCTCTCTG
1 GTGCTCTCTG
309 TTACCCAGCA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.01
23 58 0.84
25 10 0.14
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:301 original size:69 final size:68
Alignment explanation
Indices: 218--353 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 68
208 CTCTCTGTTA
* *
218 TTAGCACTATGTGTGCTCTCTG-A-CTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACT
1 TTAGCACTATGTGTGCTCTCTGTACCCAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-GTACT
281 CTCTAT
63 CTCTAT
* *
287 TTAGCACTGTGTGTGCTCTCTGTTACCCAGCACTTATGTGCTCTCTGTTAGTATTTTGGTACTCT
1 TTAGCACTATGTGTGCTCTCTG-TACCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCT
352 CT
65 CT
354 GTTTGTTCTG
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
69 30 0.50
70 10 0.17
71 14 0.23
72 6 0.10
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (68 bp):
TTAGCACTATGTGTGCTCTCTGTACCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTC
TAT
Found at i:3664 original size:17 final size:19
Alignment explanation
Indices: 3620--3667 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
3610 CCCCTAAATC
3620 TTCC-TTTT-ATTTTATAT
1 TTCCATTTTAATTTTATAT
*
3637 TTCCTTTTTAATTTTAT-T
1 TTCCATTTTAATTTTATAT
3655 TT-CATTTTAATTT
1 TTCCATTTTAATTT
3668 GGCCCTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 14 0.50
18 7 0.25
19 7 0.25
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCCATTTTAATTTTATAT
Found at i:8901 original size:18 final size:17
Alignment explanation
Indices: 8859--8907 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
8849 GATTTCACCC
*
8859 AAAAAGAAGAAAAAGAA
1 AAAAAAAAGAAAAAGAA
8876 AAAGAAAAAGAAAAAGAA
1 AAA-AAAAAGAAAAAGAA
* *
8894 AACAAAAACAAAAA
1 AAAAAAAAGAAAAA
8908 AGGAGAGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAAGAA
Found at i:8907 original size:6 final size:6
Alignment explanation
Indices: 8865--8895 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
8855 ACCCAAAAAG
8865 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A
8896 CAAAAACAAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:8907 original size:12 final size:11
Alignment explanation
Indices: 8859--8908 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
8849 GATTTCACCC
*
8859 AAAAAGAAGAA
1 AAAAAAAAGAA
8870 AAAGAAAAAGAA
1 AAA-AAAAAGAA
8882 AAAGAAAAAGAA
1 AAA-AAAAAGAA
* *
8894 AACAAAAACAA
1 AAAAAAAAGAA
8905 AAAA
1 AAAA
8909 GGAGAGGTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 13 0.38
12 21 0.62
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:9989 original size:49 final size:49
Alignment explanation
Indices: 9846--10185 Score: 231
Period size: 50 Copynumber: 6.9 Consensus size: 49
9836 ACCAAGGAAA
* *
9846 CATGAATG-TTTGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCT-GATAC
1 CATGAA-GATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTAG-TAC
* * * * * * * *
9895 CTTAAAAGATGTGATAAGAAAAGGTTGAGGCCGTAAAGATGAACCTAGTAC
1 CAT-GAAGATTTGA-AGGGAAAGGTTGAGGCCGCAACGGTGAACCTAGTAC
* * *
9946 CATGAAGATTTGAAAGGAAAGGTTGAGACCGCAACGGTAAACCTAGTAC
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTAGTAC
* * * * * * **
9995 CTTAGAAGATGTGATGGGAAAGGTTGATGCCGTAACGGCGAACCCGGTAC
1 CAT-GAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTAGTAC
* **
10045 CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTAC
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTAGTAC
* * * * * * * *
10094 CTTAGAAGATGTGATA-GGAGAGATTGAGGCCGTAACGGCGAA-TTCGGTAC
1 CAT-GAAGATTTGA-AGGGAAAGGTTGAGGCCGCAACGGTGAACCT-AGTAC
** * * * *
10144 CATGAA-ACATGATGAGAAAGGTTGAGGCTGCAACGATGAACC
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACC
10186 CGAAACCATG
Statistics
Matches: 223, Mismatches: 58, Indels: 20
0.74 0.19 0.07
Matches are distributed among these distances:
48 23 0.10
49 80 0.36
50 89 0.40
51 30 0.13
52 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (49 bp):
CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTAGTAC
Found at i:10021 original size:50 final size:50
Alignment explanation
Indices: 9861--10131 Score: 253
Period size: 50 Copynumber: 5.4 Consensus size: 50
9851 ATGTTTGAAG
* * *
9861 GGAAAGGTTGAGGCCGCAACAGCGAACCT-GATACCTTAAAAGATGTGATAA
1 GGAAAGGTTGAGGCCGCAACGGTGAACCTAG-TACCTTAGAAGATGTGAT-A
* * * * * * *
9912 GAAAAGGTTGAGGCCGTAAAGATGAACCTAGTACCAT-GAAGATTTGAAA
1 GGAAAGGTTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATGTGATA
* * *
9961 GGAAAGGTTGAGACCGCAACGGTAAACCTAGTACCTTAGAAGATGTGATG
1 GGAAAGGTTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATGTGATA
* * * ** * *
10011 GGAAAGGTTGATGCCGTAACGGCGAACCCGGTACCAT-GAAGATTTGA-A
1 GGAAAGGTTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATGTGATA
* **
10059 GGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATA
1 -GGAAAGGTTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATGTGATA
* * *
10110 GGAGAGATTGAGGCCGTAACGG
1 GGAAAGGTTGAGGCCGCAACGG
10132 CGAATTCGGT
Statistics
Matches: 175, Mismatches: 40, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
49 72 0.41
50 73 0.42
51 29 0.17
52 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (50 bp):
GGAAAGGTTGAGGCCGCAACGGTGAACCTAGTACCTTAGAAGATGTGATA
Found at i:10064 original size:99 final size:98
Alignment explanation
Indices: 9846--10185 Score: 387
Period size: 99 Copynumber: 3.4 Consensus size: 98
9836 ACCAAGGAAA
* * *
9846 CATGAATG-TTTGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCTGATACCTTAAAAGATGTGAT
1 CATGAA-GATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTG-TACCTTAGAAGATGTGAT
* * ** **
9910 AAGAAAAGGTTGAGGCCGTAAAGATGAACCTAGTAC
64 -AGGAAAGGTTGAGGCCGTAACGGCGAACCCGGTAC
* * * *
9946 CATGAAGATTTGAAAGGAAAGGTTGAGACCGCAACGGTAAACCTAGTACCTTAGAAGATGTGATG
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCT-GTACCTTAGAAGATGTGATA
*
10011 GGAAAGGTTGATGCCGTAACGGCGAACCCGGTAC
65 GGAAAGGTTGAGGCCGTAACGGCGAACCCGGTAC
* *
10045 CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATA
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAA-CCTGTACCTTAGAAGATGTGATA
* * **
10110 GGAGAGATTGAGGCCGTAACGGCGAATTCGGTAC
65 GGAAAGGTTGAGGCCGTAACGGCGAACCCGGTAC
** * * * *
10144 CATGAA-ACATGATGAGAAAGGTTGAGGCTGCAACGATGAACC
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACC
10186 CGAAACCATG
Statistics
Matches: 205, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
97 2 0.01
98 27 0.13
99 119 0.58
100 56 0.27
101 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (98 bp):
CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGTACCTTAGAAGATGTGATAG
GAAAGGTTGAGGCCGTAACGGCGAACCCGGTAC
Found at i:11202 original size:13 final size:13
Alignment explanation
Indices: 11184--11208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11174 GTTTTTTTAA
11184 TTTTTAATTAATG
1 TTTTTAATTAATG
11197 TTTTTAATTAAT
1 TTTTTAATTAAT
11209 AAATATATCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:11390 original size:12 final size:12
Alignment explanation
Indices: 11373--11398 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11363 ACATCTACTG
11373 ATTTTTTTATAT
1 ATTTTTTTATAT
11385 ATTTTTTTATAT
1 ATTTTTTTATAT
11397 AT
1 AT
11399 AATATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
ATTTTTTTATAT
Found at i:11410 original size:15 final size:15
Alignment explanation
Indices: 11390--11422 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
11380 TATATATTTT
11390 TTTATATAT--AATA
1 TTTATATATCAAATA
11403 TTTATATATCAAATA
1 TTTATATATCAAATA
11418 TTTAT
1 TTTAT
11423 TTCTTCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATATCAAATA
Found at i:26536 original size:12 final size:12
Alignment explanation
Indices: 26514--26604 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
26504 ATTATTCATT
26514 AACATTGTTCGTG
1 AACA-TGTTCGTG
*
26527 AACATGTTCGTT
1 AACATGTTCGTG
*
26539 TA-ATGTTCGTG
1 AACATGTTCGTG
26550 AACATGTTCGAT-
1 AACATGTTCG-TG
* *
26562 TA-ATATTCGTG
1 AACATGTTCGTG
26573 AACATGTTCGAT-
1 AACATGTTCG-TG
* *
26585 TA-ATGTTCATG
1 AACATGTTCGTG
26596 AACATGTTC
1 AACATGTTC
26605 AATTAAGTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
10 2 0.03
11 23 0.38
12 29 0.48
13 6 0.10
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:26546 original size:23 final size:23
Alignment explanation
Indices: 26519--26610 Score: 148
Period size: 23 Copynumber: 4.0 Consensus size: 23
26509 TCATTAACAT
*
26519 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
26542 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
*
26565 TATTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
* *
26588 TGTTCATGAACATGTTCAATTAA
1 TGTTCGTGAACATGTTCGATTAA
26611 GTTAAATGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:26619 original size:23 final size:23
Alignment explanation
Indices: 26525--26627 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 23
26515 ACATTGTTCG
** **
26525 TGAACATGTTCGTTTAATGTTCG
1 TGAACATGTTCAATTAATGTTAA
* * **
26548 TGAACATGTTCGATTAATATTCG
1 TGAACATGTTCAATTAATGTTAA
* *
26571 TGAACATGTTCGATTAATGTTCA
1 TGAACATGTTCAATTAATGTTAA
26594 TGAACATGTTCAATTAA-GTTAAA
1 TGAACATGTTCAATTAATGTT-AA
*
26617 TGAATATGTTC
1 TGAACATGTTC
26628 GTGAACATTA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
22 3 0.04
23 69 0.96
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (23 bp):
TGAACATGTTCAATTAATGTTAA
Found at i:26626 original size:46 final size:46
Alignment explanation
Indices: 26525--26628 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 46
26515 ACATTGTTCG
* * * ***
26525 TGAACATGTTCGTTTAATGTTCGTGAACATGTTCGATTAATATTCG
1 TGAACATGTTCGATTAATGTTCATGAACATGTTCAATTAATATAAA
26571 TGAACATGTTCGATTAATGTTCATGAACATGTTCAATTAAGT-TAAA
1 TGAACATGTTCGATTAATGTTCATGAACATGTTCAATTAA-TATAAA
*
26617 TGAATATGTTCG
1 TGAACATGTTCG
26629 TGAACATTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 49 0.98
47 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (46 bp):
TGAACATGTTCGATTAATGTTCATGAACATGTTCAATTAATATAAA
Found at i:35767 original size:21 final size:21
Alignment explanation
Indices: 35720--35789 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
35710 AATAGTACAG
*
35720 ACTTCTACAGATACAAGTGAT
1 ACTTCTACCGATACAAGTGAT
* *
35741 ATTTCTACCGGTACAAGTGACT
1 ACTTCTACCGATACAAGTGA-T
**
35763 -CTTCTACCGA-AGCAAGTCTT
1 ACTTCTACCGATA-CAAGTGAT
35783 ACTTCTA
1 ACTTCTA
35790 TCGTTAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
20 2 0.05
21 36 0.92
22 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAT
Found at i:36553 original size:24 final size:24
Alignment explanation
Indices: 36506--36558 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
36496 CATAGAAAAA
*
36506 ATTAGCTCTCATGAGCCTAGAATG
1 ATTAGCTCTCATGAGCCTAAAATG
*
36530 GTTAGCTCTCATGAGTCC-AAAATG
1 ATTAGCTCTCATGAG-CCTAAAATG
36554 ATTAG
1 ATTAG
36559 ATCTTACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (24 bp):
ATTAGCTCTCATGAGCCTAAAATG
Found at i:39532 original size:25 final size:23
Alignment explanation
Indices: 39491--39536 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
39481 CCAATTAGGG
39491 AATTATTATTTAGATTTAATTCT
1 AATTATTATTTAGATTTAATTCT
*
39514 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
39537 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCT
Found at i:39959 original size:14 final size:13
Alignment explanation
Indices: 39934--39979 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
39924 TATTGTTTAG
39934 AAAAAAAA--GAA
1 AAAAAAAATCGAA
39945 AAAAAAAAGTCGAA
1 AAAAAAAA-TCGAA
* *
39959 AAGAAAAATTGAA
1 AAAAAAAATCGAA
39972 AAAAAAAA
1 AAAAAAAA
39980 AGAAAATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 8 0.28
13 11 0.38
14 10 0.34
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:39979 original size:19 final size:20
Alignment explanation
Indices: 39957--40025 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 20
39947 AAAAAAGTCG
39957 AAAAGA-AAAATTGAAAAAA
1 AAAAGACAAAATTGAAAAAA
*
39976 AAAA-AGAAAATTGAGGAAAAA
1 AAAAGACAAAATTGA--AAAAA
39997 AAAAGA-AAAA--GAAAAAGA
1 AAAAGACAAAATTGAAAAA-A
40015 AAAAGACAAAA
1 AAAAGACAAAA
40026 GTGTGTTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.09
18 8 0.18
19 18 0.41
21 13 0.30
22 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.06
Consensus pattern (20 bp):
AAAAGACAAAATTGAAAAAA
Found at i:39980 original size:20 final size:20
Alignment explanation
Indices: 39957--40025 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
39947 AAAAAAGTCG
39957 AAAAGAAAAATTGAAAAAAA
1 AAAAGAAAAATTGAAAAAAA
*
39977 AAAAG-AAAATTGAGGAAAAA
1 AAAAGAAAAATTGA-AAAAAA
*
39997 AAAAGAAAAA--GAAAAAGA
1 AAAAGAAAAATTGAAAAAAA
40015 AAAAGACAAAA
1 AAAAGA-AAAA
40026 GTGTGTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 10 0.23
19 14 0.33
20 15 0.35
21 4 0.09
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.06
Consensus pattern (20 bp):
AAAAGAAAAATTGAAAAAAA
Found at i:40025 original size:7 final size:6
Alignment explanation
Indices: 39937--40026 Score: 67
Period size: 6 Copynumber: 14.0 Consensus size: 6
39927 TGTTTAGAAA
* *
39937 AAAAAG AAAAA- AAAAAG TCGAAAAG AAAAATTG AAAAAA AAAAAG AAAATTGAG
1 AAAAAG AAAAAG AAAAAG --AAAAAG AAAAA--G AAAAAG AAAAAG AAAA---AG
*
39991 GAAAA- AAAAAG AAAAAG AAAAAG AAAAAG ACAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG
40027 TGTGTTTGAG
Statistics
Matches: 68, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
5 9 0.13
6 38 0.56
7 5 0.07
8 11 0.16
9 5 0.07
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.06
Consensus pattern (6 bp):
AAAAAG
Done.