Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001430.1 Kokia drynarioides strain JFW-HI SEQ_112937, 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: 58451
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:10442 original size:17 final size:17
Alignment explanation
Indices: 10420--10468 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
10410 TATAAATAAA
10420 AAATATATAAAATTATT
1 AAATATATAAAATTATT
*
10437 AAATAT-T-AAATTA-A
1 AAATATATAAAATTATT
*
10451 AAATAATATAAACTTATT
1 AAAT-ATATAAAATTATT
10469 TTTAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 2 0.08
17 11 0.44
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATATAAAATTATT
Found at i:16480 original size:65 final size:65
Alignment explanation
Indices: 16376--16501 Score: 216
Period size: 65 Copynumber: 1.9 Consensus size: 65
16366 TTGATAATCA
* *
16376 CTATAGCGTAGTATCACAGAAGTTCCTTATAAACAAGGAAATATGATGAGTAGAGAAACTTATCT
1 CTATAGCATAGTATCACAGAAGTTCCTTATAAACAAGGAAATATGATGAGTAGAAAAACTTATCT
* *
16441 CTATAGCATAGTATCACAGAAGTTTCTTATAAACAAGGAAATATGATGTGTAGAAAAACTT
1 CTATAGCATAGTATCACAGAAGTTCCTTATAAACAAGGAAATATGATGAGTAGAAAAACTT
16502 CCTTTCTTGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (65 bp):
CTATAGCATAGTATCACAGAAGTTCCTTATAAACAAGGAAATATGATGAGTAGAAAAACTTATCT
Found at i:18833 original size:29 final size:29
Alignment explanation
Indices: 18798--18864 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
18788 ACTTCCAATT
18798 AAACGACGTGCCGTTTTCATTAGAGGAAG
1 AAACGACGTGCCGTTTTCATTAGAGGAAG
18827 AAACGACGTGCCGTTTTCATTAGAGGAAG
1 AAACGACGTGCCGTTTTCATTAGAGGAAG
18856 AAACGACGT
1 AAACGACGT
18865 CGTTTCAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (29 bp):
AAACGACGTGCCGTTTTCATTAGAGGAAG
Found at i:19667 original size:20 final size:19
Alignment explanation
Indices: 19633--19693 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
19623 AATTATGTTT
*
19633 ATTTAAAATAAAATATTAA
1 ATTTAAATTAAAATATTAA
**
19652 ATTTAAATTAAAAATAAAAA
1 ATTTAAATT-AAAATATTAA
19672 ATTATAATATT-AAATATTAA
1 ATT-TAA-ATTAAAATATTAA
19692 AT
1 AT
19694 ATCTAAAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 8 0.24
20 20 0.59
21 3 0.09
22 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTAAATTAAAATATTAA
Found at i:19693 original size:7 final size:7
Alignment explanation
Indices: 19643--19700 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
19633 ATTTAAAATA
19643 AAATATT
1 AAATATT
19650 AAAT-TT
1 AAATATT
19656 -AA-ATT
1 AAATATT
* *
19661 AAAAATA
1 AAATATT
*
19668 AAAAATT
1 AAATATT
19675 ATAATATT
1 A-AATATT
19683 AAATATT
1 AAATATT
19690 AAATATCT
1 AAATAT-T
19698 AAA
1 AAA
19701 ATCACTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
5 4 0.09
6 4 0.09
7 25 0.58
8 10 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (7 bp):
AAATATT
Found at i:19694 original size:27 final size:25
Alignment explanation
Indices: 19637--19686 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
19627 ATGTTTATTT
*
19637 AAAATAAAATATTAAATTTAAATTA
1 AAAATAAAAAATTAAATTTAAATTA
19662 AAAATAAAAAATTATAATATTAAAT
1 AAAATAAAAAATTA-AAT-TTAAAT
19687 ATTAAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 3 0.14
27 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
AAAATAAAAAATTAAATTTAAATTA
Found at i:19973 original size:37 final size:33
Alignment explanation
Indices: 19884--19981 Score: 92
Period size: 37 Copynumber: 2.8 Consensus size: 33
19874 AAAATATTTG
**
19884 TTTATAAAATTCTAAAATATAT-AATTTTAAAT
1 TTTATAAAATTAAAAAATATATAAATTTTAAAT
*
19916 TTTA-AAAAGTCAAAATAATATATAAATTTTGAAAAAT
1 TTTATAAAA-TTAAAA-AATATATAAATTTT---AAAT
*
19953 TTTATGAAAATTAAAAAATATTTAAATTT
1 TTTAT-AAAATTAAAAAATATATAAATTT
19982 CAAGTAATTG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
31 4 0.08
32 7 0.13
33 7 0.13
34 6 0.11
37 20 0.38
38 5 0.09
39 4 0.08
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (33 bp):
TTTATAAAATTAAAAAATATATAAATTTTAAAT
Found at i:20080 original size:21 final size:22
Alignment explanation
Indices: 20056--20097 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
20046 AAAAGTATAT
20056 TTTTAAACTTTTTTTA-ATTTC
1 TTTTAAACTTTTTTTATATTTC
* *
20077 TTTTACATTTTTTTTATATTT
1 TTTTAAACTTTTTTTATATTT
20098 TTCACATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTAAACTTTTTTTATATTTC
Found at i:20089 original size:20 final size:20
Alignment explanation
Indices: 20064--20114 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
20054 ATTTTTAAAC
*
20064 TTTTTTTAAT-TTCTTTTACA
1 TTTTTTTAATATT-TTTCACA
*
20084 TTTTTTTTATATTTTTCACA
1 TTTTTTTAATATTTTTCACA
*
20104 TTTTTGTAATA
1 TTTTTTTAATA
20115 ATATTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTTTAATATTTTTCACA
Found at i:20211 original size:16 final size:17
Alignment explanation
Indices: 20192--20229 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
20182 TTTTTATAGA
* *
20192 TTAATTT-TTTATATTT
1 TTAATTTGTATATACTT
20208 TTAATTTGTATATACTT
1 TTAATTTGTATATACTT
20225 TTAAT
1 TTAAT
20230 AAGATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TTAATTTGTATATACTT
Found at i:20313 original size:30 final size:29
Alignment explanation
Indices: 20279--20338 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
20269 GCACTTTGTG
* *
20279 ATTGGGACAAAAGCATACTTTAAGTACCAA
1 ATTGGGACAAAA-AAAACTTTAAGTACCAA
* *
20309 ATTGGGATAAAAAAAAGTTTAAGTACCAA
1 ATTGGGACAAAAAAAACTTTAAGTACCAA
20338 A
1 A
20339 ATGAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (29 bp):
ATTGGGACAAAAAAAACTTTAAGTACCAA
Found at i:26698 original size:2 final size:2
Alignment explanation
Indices: 26693--26733 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
26683 TATATATATA
* *
26693 TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
26734 TAGTTAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.02, C:0.02, G:0.46, T:0.49
Consensus pattern (2 bp):
TG
Found at i:28999 original size:16 final size:16
Alignment explanation
Indices: 28980--29011 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28970 TCTATAGATT
28980 ATATGTCCAGATGATA
1 ATATGTCCAGATGATA
28996 ATATGTCCAGATGATA
1 ATATGTCCAGATGATA
29012 TTAGTGACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
ATATGTCCAGATGATA
Found at i:29787 original size:22 final size:22
Alignment explanation
Indices: 29762--29825 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
29752 GTCTGTGTGT
29762 ATGTATATCTATGCTTGTTGGG
1 ATGTATATCTATGCTTGTTGGG
* * *
29784 ATGTGTGTC--TG--TG-T-GT
1 ATGTATATCTATGCTTGTTGGG
29800 ATGTATATCTATGCTTGTTGGG
1 ATGTATATCTATGCTTGTTGGG
29822 ATGT
1 ATGT
29826 GTGTCTGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
16 8 0.27
17 1 0.03
18 4 0.13
20 4 0.13
21 1 0.03
22 12 0.40
ACGTcount: A:0.16, C:0.08, G:0.30, T:0.47
Consensus pattern (22 bp):
ATGTATATCTATGCTTGTTGGG
Found at i:29798 original size:38 final size:38
Alignment explanation
Indices: 29749--29835 Score: 174
Period size: 38 Copynumber: 2.3 Consensus size: 38
29739 ATAACAATAT
29749 TGTGTCTGTGTGTATGTATATCTATGCTTGTTGGGATG
1 TGTGTCTGTGTGTATGTATATCTATGCTTGTTGGGATG
29787 TGTGTCTGTGTGTATGTATATCTATGCTTGTTGGGATG
1 TGTGTCTGTGTGTATGTATATCTATGCTTGTTGGGATG
29825 TGTGTCTGTGT
1 TGTGTCTGTGT
29836 CTATTAAGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.11, C:0.08, G:0.32, T:0.48
Consensus pattern (38 bp):
TGTGTCTGTGTGTATGTATATCTATGCTTGTTGGGATG
Found at i:35189 original size:281 final size:281
Alignment explanation
Indices: 34686--35251 Score: 1114
Period size: 281 Copynumber: 2.0 Consensus size: 281
34676 TCATCATTTT
34686 CCCACCATTATCCATTTCTCTACTCTCTCCTTTTTTGCAATTAAGTTAATACATTATTATCAAAC
1 CCCACCATTATCCATTTCTCTACTCTCTCCTTTTTTGCAATTAAGTTAATACATTATTATCAAAC
34751 AAGTAGTGGTTCAACAGTTGCTAATTATTGTTCCTTTTCCTCAAGGAACAGCTTAGGCTTTTTAC
66 AAGTAGTGGTTCAACAGTTGCTAATTATTGTTCCTTTTCCTCAAGGAACAGCTTAGGCTTTTTAC
34816 AAAGTACATACGGAATTTAATTACTTTCCTTCACTTTTGAATTATTTTCATTTTTTAAATAACTT
131 AAAGTACATACGGAATTTAATTACTTTCCTTCACTTTTGAATTATTTTCATTTTTTAAATAACTT
34881 TATTCTTTTTGAGAAAATATCTAGAATTACTTATAACTCCTTCTCAATCAATAAATCGGAAGATA
196 TATTCTTTTTGAGAAAATATCTAGAATTACTTATAACTCCTTCTCAATCAATAAATCGGAAGATA
34946 ACGCGCTTTAATAGACTCAAA
261 ACGCGCTTTAATAGACTCAAA
34967 CCCACCATTATCCATTTCTCTACTCTCTCCTTTTTTGCAATTAAGTTAATACATTATTATCAAAC
1 CCCACCATTATCCATTTCTCTACTCTCTCCTTTTTTGCAATTAAGTTAATACATTATTATCAAAC
35032 AAGTAGTGGTTCAACAGTTGCTAATTATTGTTCCTTTTCCTCAAGGAACAGCTTAGGCTTTTTAC
66 AAGTAGTGGTTCAACAGTTGCTAATTATTGTTCCTTTTCCTCAAGGAACAGCTTAGGCTTTTTAC
35097 AAAGTACATACGGAATTTAATTACTTTCCTTCACTTTTGAATTATTTTCATTTTTTAAATAACTT
131 AAAGTACATACGGAATTTAATTACTTTCCTTCACTTTTGAATTATTTTCATTTTTTAAATAACTT
* *
35162 TATTCTTTTTGAGACAATATCTAGAATTACTTATAACTCCTTCTCAATCAATAAATCGGAGGATA
196 TATTCTTTTTGAGAAAATATCTAGAATTACTTATAACTCCTTCTCAATCAATAAATCGGAAGATA
35227 ACGCGCTTTAATAGACTCAAA
261 ACGCGCTTTAATAGACTCAAA
35248 CCCA
1 CCCA
35252 TGTCCTCCTG
Statistics
Matches: 283, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
281 283 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (281 bp):
CCCACCATTATCCATTTCTCTACTCTCTCCTTTTTTGCAATTAAGTTAATACATTATTATCAAAC
AAGTAGTGGTTCAACAGTTGCTAATTATTGTTCCTTTTCCTCAAGGAACAGCTTAGGCTTTTTAC
AAAGTACATACGGAATTTAATTACTTTCCTTCACTTTTGAATTATTTTCATTTTTTAAATAACTT
TATTCTTTTTGAGAAAATATCTAGAATTACTTATAACTCCTTCTCAATCAATAAATCGGAAGATA
ACGCGCTTTAATAGACTCAAA
Found at i:35451 original size:21 final size:20
Alignment explanation
Indices: 35427--35516 Score: 92
Period size: 21 Copynumber: 4.3 Consensus size: 20
35417 TATATTGTTA
35427 TTTTGGTGTTATTTTTTACTG
1 TTTTGGTGTT-TTTTTTACTG
* *
35448 TTTTGGTTGCTATTTTTTGCTG
1 TTTTGG-TG-TTTTTTTTACTG
* *
35470 TTTTGCTG-TTTTTTTACTA
1 TTTTGGTGTTTTTTTTACTG
*
35489 TTTTGATGATTTTTTTTACTG
1 TTTTGGTG-TTTTTTTTACTG
35510 TTTTGGT
1 TTTTGGT
35517 TGTTGTTTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
19 15 0.27
21 24 0.43
22 16 0.29
23 1 0.02
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.67
Consensus pattern (20 bp):
TTTTGGTGTTTTTTTTACTG
Found at i:35549 original size:24 final size:24
Alignment explanation
Indices: 35522--35573 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
35512 TTGGTTGTTG
35522 TTTTGGTGCTATTTTTGCTATTAT
1 TTTTGGTGCTATTTTTGCTATTAT
* *
35546 TTTTGTTGCTATTTTTGTTATTAT
1 TTTTGGTGCTATTTTTGCTATTAT
35570 TTTT
1 TTTT
35574 CAATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.06, G:0.13, T:0.69
Consensus pattern (24 bp):
TTTTGGTGCTATTTTTGCTATTAT
Found at i:35563 original size:12 final size:12
Alignment explanation
Indices: 35522--35564 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
35512 TTGGTTGTTG
*
35522 TTTTGGTGCTAT
1 TTTTGTTGCTAT
* **
35534 TTTTGCTATTAT
1 TTTTGTTGCTAT
35546 TTTTGTTGCTAT
1 TTTTGTTGCTAT
35558 TTTTGTT
1 TTTTGTT
35565 ATTATTTTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.09, C:0.07, G:0.16, T:0.67
Consensus pattern (12 bp):
TTTTGTTGCTAT
Found at i:35570 original size:12 final size:12
Alignment explanation
Indices: 35531--35607 Score: 66
Period size: 12 Copynumber: 6.5 Consensus size: 12
35521 GTTTTGGTGC
*
35531 TATTTTTGCTAT
1 TATTTTTGTTAT
**
35543 TATTTTTGTTGC
1 TATTTTTGTTAT
35555 TATTTTTGTTAT
1 TATTTTTGTTAT
**
35567 TATTTTT-CAAT
1 TATTTTTGTTAT
*
35578 TATTTTTGTTGT
1 TATTTTTGTTAT
* * *
35590 TGTTTTGGTTGT
1 TATTTTTGTTAT
35602 TATTTT
1 TATTTT
35608 AGTTGTTTGG
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
11 9 0.18
12 42 0.82
ACGTcount: A:0.13, C:0.04, G:0.13, T:0.70
Consensus pattern (12 bp):
TATTTTTGTTAT
Found at i:35587 original size:35 final size:36
Alignment explanation
Indices: 35531--35607 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 36
35521 GTTTTGGTGC
* *
35531 TATTTTTGCTATTATTTTTGTTGCTATTTTTGTTAT
1 TATTTTTGCAATTATTTTTGTTGCTATTTTGGTTAT
* * *
35567 TATTTTT-CAATTATTTTTGTTGTTGTTTTGGTTGT
1 TATTTTTGCAATTATTTTTGTTGCTATTTTGGTTAT
35602 TATTTT
1 TATTTT
35608 AGTTGTTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 29 0.81
36 7 0.19
ACGTcount: A:0.13, C:0.04, G:0.13, T:0.70
Consensus pattern (36 bp):
TATTTTTGCAATTATTTTTGTTGCTATTTTGGTTAT
Found at i:35604 original size:24 final size:24
Alignment explanation
Indices: 35510--35614 Score: 72
Period size: 24 Copynumber: 4.5 Consensus size: 24
35500 TTTTTTACTG
* *
35510 TTTTGGTTGTTGTTTTGG-TGCTA
1 TTTTTGTTGTTATTTTGGTTGCTA
* * *
35533 TTTTTGCTATTATTTTTGTTGCTA
1 TTTTTGTTGTTATTTTGGTTGCTA
* ***
35557 TTTTTGTTATTATTTT--TCAATTA
1 TTTTTGTTGTTATTTTGGT-TGCTA
* *
35580 TTTTTGTTGTTGTTTTGGTTGTTA
1 TTTTTGTTGTTATTTTGGTTGCTA
*
35604 TTTTAGTTGTT
1 TTTTTGTTGTT
35615 TGGATGTTAT
Statistics
Matches: 64, Mismatches: 14, Indels: 7
0.75 0.16 0.08
Matches are distributed among these distances:
22 1 0.02
23 29 0.45
24 33 0.52
25 1 0.02
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.68
Consensus pattern (24 bp):
TTTTTGTTGTTATTTTGGTTGCTA
Found at i:35629 original size:21 final size:21
Alignment explanation
Indices: 35588--35627 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
35578 TATTTTTGTT
*
35588 GTTGTTTTGGTTGTTATTTTA
1 GTTGTTTTGGATGTTATTTTA
35609 GTTG-TTTGGATGTTATTTT
1 GTTGTTTTGGATGTTATTTT
35628 TATGCGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.10, C:0.00, G:0.25, T:0.65
Consensus pattern (21 bp):
GTTGTTTTGGATGTTATTTTA
Found at i:35946 original size:13 final size:14
Alignment explanation
Indices: 35928--35960 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35918 ATTATTCACA
*
35928 TTATTTC-TCTTTT
1 TTATTTCATCATTT
35941 TTATTTCATCATTT
1 TTATTTCATCATTT
35955 TTATTT
1 TTATTT
35961 ATTTATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTCATCATTT
Found at i:45056 original size:2 final size:2
Alignment explanation
Indices: 45049--45075 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45039 TCTCATTATC
45049 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
45076 TGGATTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46223 original size:19 final size:20
Alignment explanation
Indices: 46201--46250 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
46191 AAATTACAAT
46201 AAAAATTTAAAATAATTA-A
1 AAAAATTTAAAATAATTATA
* *
46220 AAAAATTCAAAATATTTATA
1 AAAAATTTAAAATAATTATA
*
46240 AAAGATTTAAA
1 AAAAATTTAAA
46251 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAATTTAAAATAATTATA
Found at i:46319 original size:21 final size:22
Alignment explanation
Indices: 46271--46320 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
46261 TAAAAGTATA
46271 AAAATTCTAAAAATATGTAAAA-
1 AAAATT-TAAAAATATGTAAAAT
46293 AAAATTTAAAAAT-T-TAAAAT
1 AAAATTTAAAAATATGTAAAAT
46313 AATAATTT
1 AA-AATTT
46321 TGAAACCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.19
20 3 0.12
21 12 0.46
22 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATTTAAAAATATGTAAAAT
Found at i:50619 original size:16 final size:14
Alignment explanation
Indices: 50576--50631 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
50566 TCTTGTTCGG
*
50576 ATCAAAACTAAAAT
1 ATCAAAACTAAAAA
*
50590 ATCAAAATTCAAAAA
1 ATCAAAACT-AAAAA
50605 ACTCAAAACT-AAAA
1 A-TCAAAACTAAAAA
50619 AT-AAAA-TAAAAA
1 ATCAAAACTAAAAA
50631 A
1 A
50632 ACTAAAACAG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.03
12 9 0.25
13 1 0.03
14 13 0.36
15 5 0.14
16 7 0.19
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (14 bp):
ATCAAAACTAAAAA
Found at i:51674 original size:13 final size:14
Alignment explanation
Indices: 51651--51681 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
51641 AGAGTCAAGA
51651 TAAAAATATAAATT
1 TAAAAATATAAATT
51665 TAAAAA-ATAAATT
1 TAAAAATATAAATT
51678 TAAA
1 TAAA
51682 CAAAAAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAAATATAAATT
Found at i:52739 original size:3 final size:3
Alignment explanation
Indices: 52731--52759 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
52721 GCGTGTGGGA
52731 TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
52760 ATGATGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TGT
Found at i:57587 original size:16 final size:16
Alignment explanation
Indices: 57556--57590 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
57546 AAATAATATT
**
57556 TTAAAAATAATGAAAA
1 TTAAAAATAAAAAAAA
57572 TTAAAAATAAAAAAAA
1 TTAAAAATAAAAAAAA
57588 TTA
1 TTA
57591 TAGTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TTAAAAATAAAAAAAA
Done.