Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002685.1 Kokia drynarioides strain JFW-HI SEQ_114952, 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: 85471
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Warning! 163 characters in sequence are not A, C, G, or T
Found at i:925 original size:18 final size:19
Alignment explanation
Indices: 893--932 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
883 ATTTGTGATC
893 AAAATTGAAAGTGGAAGTG
1 AAAATTGAAAGTGGAAGTG
* *
912 AAAA-TGAAATTGGAATTG
1 AAAATTGAAAGTGGAAGTG
930 AAA
1 AAA
933 GTGATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.23
Consensus pattern (19 bp):
AAAATTGAAAGTGGAAGTG
Found at i:3553 original size:29 final size:29
Alignment explanation
Indices: 3496--3553 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
3486 AATAGAATTT
* *
3496 AAATAATAAAAGATAATTATTCACCAAAA
1 AAATAAGAAAAGATAATTATACACCAAAA
3525 AAATAAGAAAAGATAATT-TAC-CCAAAA
1 AAATAAGAAAAGATAATTATACACCAAAA
3552 AA
1 AA
3554 GAGATAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 8 0.30
28 2 0.07
29 17 0.63
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (29 bp):
AAATAAGAAAAGATAATTATACACCAAAA
Found at i:7733 original size:33 final size:33
Alignment explanation
Indices: 7691--7758 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
7681 GTAATGCTTA
* *
7691 CACAACAATGAACCAGGTACATCCTTCTCCTAG
1 CACAACAATGAAACAGGTACAACCTTCTCCTAG
7724 CACAACAATGAAACAGGTACAACCTTCTCCTAG
1 CACAACAATGAAACAGGTACAACCTTCTCCTAG
7757 CA
1 CA
7759 TGATGCCTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.32, G:0.12, T:0.19
Consensus pattern (33 bp):
CACAACAATGAAACAGGTACAACCTTCTCCTAG
Found at i:11442 original size:18 final size:18
Alignment explanation
Indices: 11419--11483 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
11409 CTCACTTATG
11419 TTTCTTTCTCTCTTCTTC
1 TTTCTTTCTCTCTTCTTC
* *
11437 TTTCTTTTTCTCCCTTTTTCC
1 TTTC--TTTCTCTCTTCTT-C
11458 TTT-TTTCTCT-TTCTTTTC
1 TTTCTTTCTCTCTTC--TTC
11476 TTTCTTTC
1 TTTCTTTC
11484 CTTTATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
17 2 0.05
18 14 0.38
19 6 0.16
20 11 0.30
21 4 0.11
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTCTCTCTTCTTC
Found at i:11448 original size:20 final size:19
Alignment explanation
Indices: 11423--11482 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
11413 CTTATGTTTC
11423 TTTCTCTCTTCTTCTTTCTT
1 TTTCTCTCTT-TTCTTTCTT
*
11443 TTTCTCCCTTTTTCCTTT-TT
1 TTTCTCTC-TTTT-CTTTCTT
* *
11463 TCTCTTTCTTTTCTTTCTT
1 TTTCTCTCTTTTCTTTCTT
11482 T
1 T
11483 CCTTTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 4 0.12
19 7 0.21
20 16 0.48
21 6 0.18
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCTCTCTTTTCTTTCTT
Found at i:11487 original size:18 final size:17
Alignment explanation
Indices: 11437--11497 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 17
11427 TCTCTTCTTC
*
11437 TTTCTTTTTCTCCCTT-T
1 TTTCTTTTT-TCCTTTCT
*
11454 TTCCTTTTTTCTCTTTCT
1 TTTCTTTTTTC-CTTTCT
*
11472 TTTCTTTCTTTCCTTTATT
1 TTTCTTT-TTTCCTTT-CT
11491 TTTCTTT
1 TTTCTTT
11498 GCAGCAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 2 0.06
17 11 0.31
18 11 0.31
19 12 0.33
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTCTTTTTTCCTTTCT
Found at i:27350 original size:10 final size:11
Alignment explanation
Indices: 27323--27387 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
27313 ATACTTTAAT
*
27323 TAATTGTTTTA
1 TAATTATTTTA
27334 TAATTATTTTA
1 TAATTATTTTA
27345 -AATTA-TTTA
1 TAATTATTTTA
** *
27354 TTATATTAAATGA
1 -TA-ATTATTTTA
*
27367 TAATTATTTTT
1 TAATTATTTTA
27378 TAATTATTTT
1 TAATTATTTT
27388 TTATAACAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
9 4 0.09
10 5 0.12
11 26 0.60
12 6 0.14
13 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (11 bp):
TAATTATTTTA
Found at i:33352 original size:62 final size:62
Alignment explanation
Indices: 33280--33402 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
33270 AAAATTGCTC
33280 CCAAGAAAAGTGTTTTTGTC-TTTCAAATGTACGTGTCAAAAAAG-AAAATTCGAATTGAAACT
1 CCAAGAAAAGTGTTTTTG-CGTTTCAAATGTACGTGTCAAAAAAGAAAAATT-GAATTGAAACT
33342 CCAAGAAAAGTGTTTTTGCGTTTCAAATGTACGTGTCAAAAAAGAAAAATTGAATTGAAAC
1 CCAAGAAAAGTGTTTTTGCGTTTCAAATGTACGTGTCAAAAAAGAAAAATTGAATTGAAAC
33403 ATAACAGTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
61 1 0.02
62 52 0.88
63 6 0.10
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (62 bp):
CCAAGAAAAGTGTTTTTGCGTTTCAAATGTACGTGTCAAAAAAGAAAAATTGAATTGAAACT
Found at i:34589 original size:19 final size:19
Alignment explanation
Indices: 34565--34606 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
34555 CGTTAAGGAT
34565 AATTTAAAA-TATAAAATAA
1 AATTTAAAATTATAAAA-AA
*
34584 AATTTAAAATTTTAAAAAA
1 AATTTAAAATTATAAAAAA
34603 AATT
1 AATT
34607 AAGGGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTTAAAATTATAAAAAA
Found at i:37228 original size:7 final size:8
Alignment explanation
Indices: 37208--37240 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
37198 TATTTTCTCT
37208 TTTTTATAA
1 TTTTTA-AA
37217 TTTTTAAA
1 TTTTTAAA
37225 TTTTTAAA
1 TTTTTAAA
37233 TTTTTAAA
1 TTTTTAAA
37241 AAAAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTTAAA
Found at i:41791 original size:32 final size:33
Alignment explanation
Indices: 41719--41800 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 33
41709 AAAAGACTAC
* *
41719 TTATTTT-TTACTATTTTTGTGCTTTTTTTTTTA
1 TTATTTTGTTACTATTTTTGTGC-TTGTTTTTCA
*
41752 TTGTTTTGTTACTATTTTCT-TG-TTGTTTTTCA
1 TTATTTTGTTACTATTTT-TGTGCTTGTTTTTCA
* *
41784 TTATTTTGCTACAATTT
1 TTATTTTGTTACTATTT
41801 CGTTATTATG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
32 22 0.54
33 6 0.15
34 12 0.29
35 1 0.02
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.70
Consensus pattern (33 bp):
TTATTTTGTTACTATTTTTGTGCTTGTTTTTCA
Found at i:43974 original size:10 final size:10
Alignment explanation
Indices: 43961--44017 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
43951 TTTTCTATAC
43961 TTTTAATAAT
1 TTTTAATAAT
43971 TTTTAA-AA-
1 TTTTAATAAT
43979 TTTTAAT-AT
1 TTTTAATAAT
*
43988 TTTT-TTGAAT
1 TTTTAAT-AAT
43998 TTTTAA-AAT
1 TTTTAATAAT
*
44007 TTTTAAAAAT
1 TTTTAATAAT
44017 T
1 T
44018 AATTAATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
8 8 0.21
9 15 0.38
10 16 0.41
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:43984 original size:18 final size:18
Alignment explanation
Indices: 43961--44014 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 18
43951 TTTTCTATAC
43961 TTTTAATAATTTTTAAAA
1 TTTTAATAATTTTTAAAA
* * *
43979 TTTTAATATTTTTTTGAAT
1 TTTTAATA-ATTTTTAAAA
43998 TTTTAA-AATTTTTAAAA
1 TTTTAATAATTTTTAAAA
44015 ATTAATTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 7 0.24
18 9 0.31
19 13 0.45
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTAATAATTTTTAAAA
Found at i:44007 original size:9 final size:9
Alignment explanation
Indices: 43961--44014 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
43951 TTTTCTATAC
43961 TTTTAATAAT
1 TTTTAA-AAT
43971 TTTTAAAA-
1 TTTTAAAAT
*
43979 TTTTAATATT
1 TTTTAA-AAT
**
43989 TTTTTGAAT
1 TTTTAAAAT
43998 TTTTAAAAT
1 TTTTAAAAT
44007 TTTTAAAA
1 TTTTAAAA
44015 ATTAATTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
8 6 0.17
9 20 0.56
10 10 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:52995 original size:24 final size:25
Alignment explanation
Indices: 52954--53000 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
52944 TACTTTCTCA
52954 TCTTCTTCATTCTCTCTG-TTTCTT
1 TCTTCTTCATTCTCTCTGATTTCTT
*
52978 TCTTCTT-TTTCTCTTCTGATTTC
1 TCTTCTTCATTCTC-TCTGATTTC
53001 CCTTCGCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.04, C:0.28, G:0.04, T:0.64
Consensus pattern (25 bp):
TCTTCTTCATTCTCTCTGATTTCTT
Found at i:77659 original size:29 final size:29
Alignment explanation
Indices: 77627--78018 Score: 355
Period size: 29 Copynumber: 13.4 Consensus size: 29
77617 GAAAAAGAGA
*
77627 TTTTGGAGGTTCGGGGGTAAAAATGGAAT
1 TTTTGGAAGTTCGGGGGTAAAAATGGAAT
* *** **
77656 TTTTGGAAATTTTAGGGTCAAAAATGGCTT
1 TTTTGGAAGTTCGGGGGT-AAAAATGGAAT
**
77686 TTTTGGAAGTTTAGGGGTAAAAATGGAAT
1 TTTTGGAAGTTCGGGGGTAAAAATGGAAT
* * * * *
77715 TTTTTGAAGTTTTGAGGTTTAAAATGTG-A-
1 TTTTGGAAG-TTCGGGGGTAAAAATG-GAAT
77744 TTTTGGAAGTTCGGGGGTAAAAATGGAAT
1 TTTTGGAAGTTCGGGGGTAAAAATGGAAT
** *
77773 TTTTGGAAGTTTTGGGGTCAAAAATGGGAT
1 TTTTGGAAGTTCGGGGGT-AAAAATGGAAT
* *
77803 TTTTGGAAGTTTGGGGGT-AAAATGGAAC
1 TTTTGGAAGTTCGGGGGTAAAAATGGAAT
** *
77831 TTTTGGAAGTT-TTGGGTAAAAAATGGGAT
1 TTTTGGAAGTTCGGGGGT-AAAAATGGAAT
* *
77860 TATTGGAAGTTCGGGGG-AAAAAGGGTAAT
1 TTTTGGAAGTTCGGGGGTAAAAATGG-AAT
**** *
77889 TTTTGGAAGTTTTAAGGTAAAAAATGGGAT
1 TTTTGGAAGTTCGGGGGT-AAAAATGGAAT
*
77919 TTTTGGAAGTTCGAGGGTAAAAATGGAAT
1 TTTTGGAAGTTCGGGGGTAAAAATGGAAT
*
77948 TTTTGGAAGTTTC-GGGGTCAAAAATGGGAT
1 TTTTGGAAG-TTCGGGGGT-AAAAATGGAAT
* *
77978 TTTTGAAAGTTCGGGAGTAAAAATGGAAT
1 TTTTGGAAGTTCGGGGGTAAAAATGGAAT
78007 TTTTGGATAGTT
1 TTTTGGA-AGTT
78019 TAGGGACCTC
Statistics
Matches: 293, Mismatches: 54, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
27 5 0.02
28 39 0.13
29 128 0.44
30 113 0.39
31 8 0.03
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (29 bp):
TTTTGGAAGTTCGGGGGTAAAAATGGAAT
Found at i:77705 original size:59 final size:58
Alignment explanation
Indices: 77627--78023 Score: 489
Period size: 59 Copynumber: 6.8 Consensus size: 58
77617 GAAAAAGAGA
* * **
77627 TTTTGGAGGTTCGGGGGTAAAAATGGAATTTTTGGAAATTTTAGGGTCAAAAATGGCTT
1 TTTTGGAAGTTC-GGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGGAT
* * ** *
77686 TTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTTGAAGTTTT-GAGGTTTAAAATGTGA-
1 TTTTGGAAG-TTCGGGGTAAAAATGGAATTTTTGGAAGTTTTAG-GGTCAAAAATGGGAT
*
77744 TTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGAT
1 TTTTGGAAGTTC-GGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGGAT
* * *
77803 TTTTGGAAGTTTGGGGGT-AAAATGGAACTTTTGGAAGTTTT-GGGTAAAAAATGGGAT
1 TTTTGGAAG-TTCGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGGAT
* * * * *
77860 TATTGGAAGTTCGGGGGAAAAAGGGTAATTTTTGGAAGTTTTAAGGTAAAAAATGGGAT
1 TTTTGGAAGTTCGGGGTAAAAATGG-AATTTTTGGAAGTTTTAGGGTCAAAAATGGGAT
**
77919 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGAT
1 TTTTGGAAGTTCG-GGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGGAT
*
77978 TTTTGAAAGTTCGGGAGTAAAAATGGAATTTTTGGATAG-TTTAGGG
1 TTTTGGAAGTTCGGG-GTAAAAATGGAATTTTTGGA-AGTTTTAGGG
78024 ACCTCCAAGG
Statistics
Matches: 293, Mismatches: 33, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
56 6 0.02
57 31 0.11
58 88 0.30
59 152 0.52
60 16 0.05
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (58 bp):
TTTTGGAAGTTCGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGGAT
Found at i:79057 original size:3 final size:3
Alignment explanation
Indices: 79004--79038 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
78994 CGGGTTTTCT
*
79004 TTA TTA TTAA TTA TTA ATA TTA TTA TTA TTA TTA T
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA T
79039 CAAAACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:79825 original size:6 final size:6
Alignment explanation
Indices: 79810--79929 Score: 65
Period size: 6 Copynumber: 20.7 Consensus size: 6
79800 TGTAATTGAT
* * *
79810 TTTAAA TTTAAG TTTAAA ATT--A TTTCAAA TTTAAA -CT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* * * ** *
79855 CTT-AA TTTAAA TTTAAA -ATAAA TTTAAA TTAAAAAA AATGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT--TAAA TTTAAA TTTAAA
* *
79903 TTTAAA TTTAAA -GTAAA TTTAAT TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
79930 GAAATAAATC
Statistics
Matches: 83, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
4 5 0.06
5 14 0.17
6 57 0.69
7 4 0.05
8 3 0.04
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:79854 original size:27 final size:28
Alignment explanation
Indices: 79822--79886 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
79812 TAAATTTAAG
*
79822 TTTAAAATT-ATTTCAAATTTAAACT-AA
1 TTTAAAATTAATTT-AAATTTAAAATAAA
*
79849 TTTAAACTTAATTTAAATTTAAAATAAA
1 TTTAAAATTAATTTAAATTTAAAATAAA
79877 TTT-AAATTAA
1 TTTAAAATTAA
79887 AAAAAATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (28 bp):
TTTAAAATTAATTTAAATTTAAAATAAA
Found at i:79862 original size:11 final size:11
Alignment explanation
Indices: 79837--79870 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
79827 AATTATTTCA
79837 AATTTAAAC-T
1 AATTTAAACTT
79847 AATTTAAACTT
1 AATTTAAACTT
*
79858 AATTTAAATTT
1 AATTTAAACTT
79869 AA
1 AA
79871 AATAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAACTT
Found at i:79867 original size:17 final size:17
Alignment explanation
Indices: 79847--79943 Score: 66
Period size: 17 Copynumber: 6.1 Consensus size: 17
79837 AATTTAAACT
* *
79847 AATTTAAACTTAATTTA
1 AATTTAAAATAAATTTA
79864 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* *
79881 AA-TTAAAA-AAA-ATG
1 AATTTAAAATAAATTTA
79895 AA-TT----TAAATTTA
1 AATTTAAAATAAATTTA
*
79907 AATTTAAAGTAAATTTA
1 AATTTAAAATAAATTTA
* *
79924 ATTTTAGAAATAAATCTA
1 AATTTA-AAATAAATTTA
79942 AA
1 AA
79944 ACTCATTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
11 3 0.05
12 3 0.05
13 2 0.03
14 5 0.08
15 3 0.05
16 6 0.10
17 30 0.48
18 10 0.16
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:79876 original size:11 final size:11
Alignment explanation
Indices: 79862--79924 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
79852 AAACTTAATT
79862 TAAATTTAAAA
1 TAAATTTAAAA
*
79873 TAAATTTAAAT
1 TAAATTTAAAA
*
79884 TAAA--AAAAA
1 TAAATTTAAAA
* *
79893 TGAATTTAAATT
1 TAAATTTAAA-A
*
79905 TAAATTTAAAG
1 TAAATTTAAAA
79916 TAAATTTAA
1 TAAATTTAA
79925 TTTTAGAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
9 6 0.15
11 26 0.63
12 9 0.22
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:80062 original size:22 final size:22
Alignment explanation
Indices: 80037--80107 Score: 52
Period size: 28 Copynumber: 3.0 Consensus size: 22
80027 ATTTTTGAAC
80037 TTAAAATTAGATTACTAATATT
1 TTAAAATTAGATTACTAATATT
* * *
80059 TTAAGAGTTTGATTTCTTATTTTATATT
1 TTAA-AATTAGATTAC-TA----ATATT
*
80087 TTAAAATTAGATTACTTATAT
1 TTAAAATTAGATTACTAATAT
80108 AATCTATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
22 8 0.22
23 8 0.22
24 2 0.06
26 1 0.03
27 8 0.22
28 9 0.25
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (22 bp):
TTAAAATTAGATTACTAATATT
Done.