Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006246.1 Kokia drynarioides strain JFW-HI SEQ_120817, 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: 63772
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:7774 original size:11 final size:11
Alignment explanation
Indices: 7758--7783 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7748 CCCCACATAA
7758 TAAATTTGTTT
1 TAAATTTGTTT
7769 TAAATTTGTTT
1 TAAATTTGTTT
7780 TAAA
1 TAAA
7784 CATCTATTAT
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:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TAAATTTGTTT
Found at i:8036 original size:40 final size:41
Alignment explanation
Indices: 7987--8105 Score: 150
Period size: 42 Copynumber: 2.9 Consensus size: 41
7977 TTGAATTAAT
* * *
7987 ACACTGGCTTATAGCCCACTAAGCCGAAGCTTGAGTTT-TG
1 ACACCGGCTTATAGCCTACTAAGCCGTAGCTTGAGTTTATG
* *
8027 ACACCGGCTTATAGCCTGCTAAGCCGTAGCTTGAGTTTTATT
1 ACACCGGCTTATAGCCTACTAAGCCGTAGCTTGAG-TTTATG
** *
8069 ACACCGGCACATAGCCTACTAAACCGTAGCTTGAGTT
1 ACACCGGCTTATAGCCTACTAAGCCGTAGCTTGAGTT
8106 GATTCAAACA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 31 0.46
41 5 0.07
42 32 0.47
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (41 bp):
ACACCGGCTTATAGCCTACTAAGCCGTAGCTTGAGTTTATG
Found at i:8205 original size:2 final size:2
Alignment explanation
Indices: 8198--8237 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
8188 AACAATTAAC
8198 AT AT AT AT AT AT 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 AT AT AT AT AT AT
8238 GTAGCTTGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8354 original size:144 final size:144
Alignment explanation
Indices: 8094--8355 Score: 479
Period size: 144 Copynumber: 1.8 Consensus size: 144
8084 CTACTAAACC
*
8094 GTAGCTTGAGTTGATTCAAACAAAACTACACATTACTTTTCTTTTTCACATTCAACAACCACATT
1 GTAGCTTGAGTTGATTCAAACAAAACTACACAATACTTTTCTTTTTCACATTCAACAACCACATT
* *
8159 TATATCCAAGCATTCCAAAAAATGAGCTTAACAATTAACATATATATATATATATATATATATAT
66 TATATCCAAGCAATCCAAAAAATGAGCTTAACAATTAACAAATATATATATATATATATATATAT
8224 ATATATATATATAT
131 ATATATATATATAT
* *
8238 GTAGCTTGAGTTGATTCAAACATAACTACACAATACTTTTCTTTTTCTCATTCAACAACCACATT
1 GTAGCTTGAGTTGATTCAAACAAAACTACACAATACTTTTCTTTTTCACATTCAACAACCACATT
8303 TATATCCAAGCAATCCAAAAAATGAGCTTAACAATTAACAAATATATATATAT
66 TATATCCAAGCAATCCAAAAAATGAGCTTAACAATTAACAAATATATATATAT
8356 CTTTAAATAG
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 113 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (144 bp):
GTAGCTTGAGTTGATTCAAACAAAACTACACAATACTTTTCTTTTTCACATTCAACAACCACATT
TATATCCAAGCAATCCAAAAAATGAGCTTAACAATTAACAAATATATATATATATATATATATAT
ATATATATATATAT
Found at i:12083 original size:3 final size:3
Alignment explanation
Indices: 12075--12147 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
12065 TAGATACGAT
* *
12075 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
12123 TTA TTA TTT TTA TTTA TTT TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA
12148 ACTTACATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16453 original size:47 final size:41
Alignment explanation
Indices: 16344--16473 Score: 188
Period size: 41 Copynumber: 3.1 Consensus size: 41
16334 GAGCCGCAAA
* * *
16344 TCTTCCTTTAACCATATTCTCATTCTTATCTCGAGACATGAG
1 TCTTCC-TTAATCATAATCTCATTCTCATCTCGAGACATGAG
* *
16386 TCTTCCTTAATCATAATCTCATTCTCATTTTGAGACATGAG
1 TCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATGAG
* *
16427 TCTTCCTTATTCATAATCTCACTCTCATCTCGAGACATGAG
1 TCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATGAG
16468 TCTTCC
1 TCTTCC
16474 ATTTATACAA
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 73 0.92
42 6 0.08
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (41 bp):
TCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATGAG
Found at i:22636 original size:19 final size:19
Alignment explanation
Indices: 22612--22659 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
22602 TGATTCTTTA
*
22612 ATGTGGTGTATTATTAATT
1 ATGTGGTGTAGTATTAATT
22631 ATGTGGTGTAGTATTAATT
1 ATGTGGTGTAGTATTAATT
22650 ATGTGGTGTA
1 ATGTGGTGTA
22660 ATACTAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (19 bp):
ATGTGGTGTAGTATTAATT
Found at i:26784 original size:24 final size:24
Alignment explanation
Indices: 26751--26811 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
26741 AACTAATAAG
*
26751 AGTTTGATTGAAACAAATAAACAA
1 AGTTTAATTGAAACAAATAAACAA
*
26775 AGTTTAATTGAAACAAATAAACAG
1 AGTTTAATTGAAACAAATAAACAA
26799 AGTTTAATTGAAA
1 AGTTTAATTGAAA
26812 GATTATTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (24 bp):
AGTTTAATTGAAACAAATAAACAA
Found at i:28745 original size:3 final size:3
Alignment explanation
Indices: 28737--28761 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28727 GAAATAGAAG
28737 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
28762 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:35070 original size:3 final size:3
Alignment explanation
Indices: 35044--35095 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
35034 ACGATAGTAG
* * *
35044 TAA TAC TAA TAG TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
35093 TAA
1 TAA
35096 CAATCCATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:38872 original size:28 final size:27
Alignment explanation
Indices: 38765--38936 Score: 76
Period size: 28 Copynumber: 6.1 Consensus size: 27
38755 ATTTTTTAAG
* * *
38765 AATAGTGGCAAAACTATAAAATTTGTAA
1 AATAGTGGC-AAACTTTAAAATCTGGAA
* ** **
38793 AACAGTGATAGAACTGAAAAATCTGGAA
1 AATAGTGGCA-AACTTTAAAATCTGGAA
* * * *
38821 AACCAATGGCAAAATTGTAGAATCTGGAA
1 AA-TAGTGGCAAACTT-TAAAATCTGGAA
*
38850 AATAGTGGCAGAACTTTAAAATCTAGAA
1 AATAGTGGCA-AACTTTAAAATCTGGAA
* * * * *
38878 ATTCAGTGGTAAAATTGTAAAATTTTTGAA
1 AAT-AGTGGCAAACTT-TAAAA-TCTGGAA
**
38908 AATAGTGGCAAAACTGCAAAATCT-GAA
1 AATAGTGGC-AAACTTTAAAATCTGGAA
38935 AA
1 AA
38937 GCACAATTGA
Statistics
Matches: 106, Mismatches: 30, Indels: 17
0.69 0.20 0.11
Matches are distributed among these distances:
27 6 0.06
28 48 0.45
29 41 0.39
30 11 0.10
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (27 bp):
AATAGTGGCAAACTTTAAAATCTGGAA
Found at i:39009 original size:29 final size:29
Alignment explanation
Indices: 38768--39025 Score: 157
Period size: 29 Copynumber: 8.9 Consensus size: 29
38758 TTTTAAGAAT
* *
38768 AGTGGCAAAACTATAAAATTTGTAAAA-C
1 AGTGGCAAAACTGTAAAATTTGGAAAATC
** * * * *
38796 AGTGATAGAACTGAAAAATCTGGAAAACC
1 AGTGGCAAAACTGTAAAATTTGGAAAATC
* * * *
38825 AATGGCAAAATTGTAGAATCTGGAAAAT-
1 AGTGGCAAAACTGTAAAATTTGGAAAATC
* * * * *
38853 AGTGGCAGAACTTTAAAATCTAGAAATTC
1 AGTGGCAAAACTGTAAAATTTGGAAAATC
* * *
38882 AGTGGTAAAATTGTAAAATTTTTGAAAAT-
1 AGTGGCAAAACTGTAAAA-TTTGGAAAATC
* * *
38911 AGTGGCAAAACTGCAAAATCT-GAAAAGCAC
1 AGTGGCAAAACTGTAAAATTTGGAAAA--TC
* * * *
38941 AATTGAAAAACTGTAAAATTCTAGAAAAT-
1 AGTGGCAAAACTGTAAAATT-TGGAAAATC
*
38970 AGTGGTAAAACTGTAAAATTTGGAAAATC
1 AGTGGCAAAACTGTAAAATTTGGAAAATC
* * * *
38999 AGTAGCAAAACTATAGAATTTGAAAAA
1 AGTGGCAAAACTGTAAAATTTGGAAAA
39026 AAAAACAAAT
Statistics
Matches: 172, Mismatches: 49, Indels: 17
0.72 0.21 0.07
Matches are distributed among these distances:
27 5 0.03
28 50 0.29
29 89 0.52
30 22 0.13
31 1 0.01
32 5 0.03
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (29 bp):
AGTGGCAAAACTGTAAAATTTGGAAAATC
Found at i:39490 original size:33 final size:32
Alignment explanation
Indices: 39439--39504 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
39429 AAAGATAAAG
*
39439 TCTATTAGGATTTGAAAAGGAGTAATTTGAAT
1 TCTATTAAGATTTGAAAAGGAGTAATTTGAAT
* *
39471 TCTACTTAAGATTTTAAAAGGATTAATTTGAAT
1 TCTA-TTAAGATTTGAAAAGGAGTAATTTGAAT
39504 T
1 T
39505 TCAAATTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.41
Consensus pattern (32 bp):
TCTATTAAGATTTGAAAAGGAGTAATTTGAAT
Found at i:42085 original size:42 final size:42
Alignment explanation
Indices: 42026--42109 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
42016 AGCATTCCTA
42026 TCTAATGGAAAAGATACTAACTTCCAGGTCCCATTGCGCATG
1 TCTAATGGAAAAGATACTAACTTCCAGGTCCCATTGCGCATG
42068 TCTAATGGAAAAGATACTAACTTCCAGGTCCCATTGCGCATG
1 TCTAATGGAAAAGATACTAACTTCCAGGTCCCATTGCGCATG
42110 AGAGCATCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
TCTAATGGAAAAGATACTAACTTCCAGGTCCCATTGCGCATG
Found at i:47154 original size:29 final size:28
Alignment explanation
Indices: 47036--47322 Score: 161
Period size: 29 Copynumber: 10.0 Consensus size: 28
47026 GTTATTATTT
* *
47036 TTGAAGAATAGTGGGAAAACTATAAAAT-
1 TTGAA-AATAGTGGCAAAACTGTAAAATC
*
47064 TTGAAAAATAGTGGCAAAATTGTAAAATC
1 TTG-AAAATAGTGGCAAAACTGTAAAATC
* * * * * *
47093 TAGAAAA-ATTGGTAGAACTGAAAAATT
1 TTGAAAATAGTGGCAAAACTGTAAAATC
*
47120 TTGAAAACTAGTGACAAAACTGTAAAATC
1 TTGAAAA-TAGTGGCAAAACTGTAAAATC
* * * * * *
47149 TGGAAAAACATTGGTAGAATTGTAAAATC
1 TTG-AAAATAGTGGCAAAACTGTAAAATC
* * * * *
47178 TAGAAAATCAGTTGCAGAATTGTAAAATT
1 TTGAAAAT-AGTGGCAAAACTGTAAAATC
* *
47207 TTGGAAAATAATGGCAAAATTGTAAAAT-
1 TT-GAAAATAGTGGCAAAACTGTAAAATC
* *
47235 TATGGAAAATAGTGGCAAAATTATAAAATC
1 T-T-GAAAATAGTGGCAAAACTGTAAAATC
* * *
47265 -TAAAAATTTAGTGGTAAAACTATAAAAT-
1 TTGAAAA--TAGTGGCAAAACTGTAAAATC
* * *
47293 TTAAAAAATAGTGGCATAACTATAAAATC
1 TT-GAAAATAGTGGCAAAACTGTAAAATC
47322 T
1 T
47323 GTAAAACGGT
Statistics
Matches: 204, Mismatches: 41, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
27 24 0.12
28 50 0.25
29 115 0.56
30 15 0.07
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (28 bp):
TTGAAAATAGTGGCAAAACTGTAAAATC
Found at i:47202 original size:58 final size:55
Alignment explanation
Indices: 47058--47265 Score: 195
Period size: 58 Copynumber: 3.6 Consensus size: 55
47048 GGGAAAACTA
* * *
47058 TAAAATTTGAAAAATAGTGGCAAAATTGTAAAATCTAG-AAAAATTGGTAGAACTG
1 TAAAATTAG-AAAATAGTGGCAAAATTGTAAAATCTGGAAAAAATTGGTAGAATTG
* * * *
47113 AAAAATTTTGAAAACTAGTGACAAAACTGTAAAATCTGGAAAAACATTGGTAGAATTG
1 TAAAA-TTAGAAAA-TAGTGGCAAAATTGTAAAATCTGGAAAAA-ATTGGTAGAATTG
* * * * *
47171 TAAAATCTAGAAAATCAGTTGCAGAATTGTAAAATTTTGGAAAATAA-TGGCAAAATTG
1 TAAAAT-TAGAAAAT-AGTGGCAAAATTGTAAAA-TCTGGAAAA-AATTGGTAGAATTG
*
47229 TAAAATTATGGAAAATAGTGGCAAAATTATAAAATCT
1 TAAAATTA--GAAAATAGTGGCAAAATTGTAAAATCT
47266 AAAAATTTAG
Statistics
Matches: 125, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
55 8 0.06
56 25 0.20
57 10 0.08
58 66 0.53
59 15 0.12
60 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.28
Consensus pattern (55 bp):
TAAAATTAGAAAATAGTGGCAAAATTGTAAAATCTGGAAAAAATTGGTAGAATTG
Found at i:47291 original size:87 final size:85
Alignment explanation
Indices: 47051--47294 Score: 244
Period size: 87 Copynumber: 2.8 Consensus size: 85
47041 GAATAGTGGG
* * *
47051 AAAACTATAAAATTTGAAAAATAGTGGCAAAATTGTAAAATCTAGAAAA-ATTGGTAGAACTGA-
1 AAAACTGTAAAATTTGGAAAATAGTGGCAAAATTGTAAAATCTAGAAAATAGTGGTAGAACT-AT
*
47114 AAAATTTTGAAAACTAGTGAC
65 AAAATTTTGAAAACTAATGAC
* * * * * * * * *
47135 AAAACTGTAAAATCTGGAAAAACATTGGTAGAATTGTAAAATCTAGAAAATCAGTTGCAGAATTG
1 AAAACTGTAAAATTTGG-AAAATAGTGGCAAAATTGTAAAATCTAGAAAAT-AGTGGTAGAACTA
*
47200 TAAAATTTTGGAAAA-TAATGGC
64 TAAAATTTT-GAAAACTAATGAC
* * *
47222 AAAATTGTAAAATTATGGAAAATAGTGGCAAAATTATAAAATCTA-AAAATTTAGTGGTAAAACT
1 AAAACTGTAAAATT-TGGAAAATAGTGGCAAAATTGTAAAATCTAGAAAA--TAGTGGTAGAACT
47286 ATAAAATTT
63 ATAAAATTT
47295 AAAAAATAGT
Statistics
Matches: 126, Mismatches: 26, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
84 14 0.11
85 28 0.22
86 4 0.03
87 71 0.56
88 9 0.07
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.28
Consensus pattern (85 bp):
AAAACTGTAAAATTTGGAAAATAGTGGCAAAATTGTAAAATCTAGAAAATAGTGGTAGAACTATA
AAATTTTGAAAACTAATGAC
Found at i:48608 original size:11 final size:10
Alignment explanation
Indices: 48587--48671 Score: 61
Period size: 10 Copynumber: 8.7 Consensus size: 10
48577 AAAATTATTA
*
48587 ATTTTTTTAT
1 ATTTTTATAT
48597 AGTTTTTATAT
1 A-TTTTTATAT
*
48608 ATTTTTAAAT
1 ATTTTTATAT
*
48618 AATTTTA-AT
1 ATTTTTATAT
* *
48627 -TTTTAAAAT
1 ATTTTTATAT
48636 AATTTTTATAT
1 -ATTTTTATAT
*
48647 ATTTTTAAAT
1 ATTTTTATAT
*
48657 -TTTTTA-AA
1 ATTTTTATAT
48665 ATTTTTA
1 ATTTTTA
48672 AAAAATTAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
8 5 0.08
9 16 0.26
10 24 0.39
11 16 0.26
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:48612 original size:10 final size:10
Alignment explanation
Indices: 48599--48673 Score: 77
Period size: 9 Copynumber: 7.8 Consensus size: 10
48589 TTTTTTATAG
*
48599 TTTTTATATA
1 TTTTTAAATA
48609 TTTTTAAATA
1 TTTTTAAATA
*
48619 ATTTT-AAT-
1 TTTTTAAATA
*
48627 TTTTAAAATAA
1 TTTTTAAAT-A
*
48638 TTTTTATATA
1 TTTTTAAATA
48648 TTTTTAAAT-
1 TTTTTAAATA
48657 TTTTTAAA-A
1 TTTTTAAATA
48666 TTTTTAAA
1 TTTTTAAA
48674 AAATTAATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
8 3 0.06
9 22 0.41
10 22 0.41
11 7 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:48647 original size:39 final size:38
Alignment explanation
Indices: 48599--48678 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 38
48589 TTTTTTATAG
48599 TTTTTATATATTTTTAAATAATTTT-AATTTTTAAAATAA
1 TTTTTATATATTTTTAAAT-ATTTTAAATTTTTAAAA-AA
*
48638 TTTTTATATATTTTTAAATTTTTTAAAATTTTTAAAAAA
1 TTTTTATATATTTTTAAATATTTT-AAATTTTTAAAAAA
48677 TT
1 TT
48679 AATTCTTGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
38 4 0.11
39 23 0.61
40 11 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (38 bp):
TTTTTATATATTTTTAAATATTTTAAATTTTTAAAAAA
Found at i:48660 original size:9 final size:9
Alignment explanation
Indices: 48584--48673 Score: 56
Period size: 9 Copynumber: 9.6 Consensus size: 9
48574 ATAAAAATTA
*
48584 TTAATTTTT
1 TTAAATTTT
* *
48593 TTATAGTTT
1 TTAAATTTT
*
48602 TTATATATTT
1 TTAAAT-TTT
*
48612 TTAAATAATT
1 TTAAAT-TTT
48622 TT-AATTTT
1 TTAAATTTT
*
48630 TAAAATAATTT
1 TTAAAT--TTT
*
48641 TTATATATTT
1 TTAAAT-TTT
48651 TTAAATTTT
1 TTAAATTTT
*
48660 TTAAAATTT
1 TTAAATTTT
48669 TTAAA
1 TTAAA
48674 AAATTAATTC
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
8 3 0.05
9 33 0.51
10 22 0.34
11 7 0.11
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (9 bp):
TTAAATTTT
Found at i:56660 original size:41 final size:41
Alignment explanation
Indices: 56613--56696 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
56603 AACAAACTTT
* *
56613 TACTAATTCAAGAAGGGTTTCATTCCTTCTCCCAAGAAATA
1 TACTAATTCAAGAAAGGTTTCACTCCTTCTCCCAAGAAATA
56654 TACTAATTCAAGAAAGGTTTCACTCCTTCTCCCAAGAAATA
1 TACTAATTCAAGAAAGGTTTCACTCCTTCTCCCAAGAAATA
56695 TA
1 TA
56697 TGGTACCGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.31
Consensus pattern (41 bp):
TACTAATTCAAGAAAGGTTTCACTCCTTCTCCCAAGAAATA
Done.