Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014938.1 Kokia drynarioides strain JFW-HI SEQ_129981, 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: 47444
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 83 characters in sequence are not A, C, G, or T
Found at i:6798 original size:7 final size:7
Alignment explanation
Indices: 6783--6862 Score: 52
Period size: 7 Copynumber: 10.0 Consensus size: 7
6773 GTCCTTCACC
*
6783 TTATGTT
1 TTATTTT
6790 TTATTTT
1 TTATTTT
6797 TTACTATTTT
1 TT---ATTTT
6807 TTATTTAT
1 TTATTT-T
6815 TTATCTTTT
1 TTA--TTTT
6824 ATTATTTT
1 -TTATTTT
6832 TTATTTT
1 TTATTTT
*
6839 TTGACTTAT
1 TT-A-TTTT
6848 TTATTTAT
1 TTATTT-T
6856 TTATTTT
1 TTATTTT
6863 CCAGCATATT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
7 24 0.40
8 17 0.28
9 6 0.10
10 13 0.22
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.75
Consensus pattern (7 bp):
TTATTTT
Found at i:6815 original size:4 final size:4
Alignment explanation
Indices: 6789--6861 Score: 61
Period size: 4 Copynumber: 19.8 Consensus size: 4
6779 CACCTTATGT
* *
6789 TTTA TTT- TTTA -CTA TTT- TTTA TTTA TTTA TCT- TTTA -TTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
6831 TTTA TTT- TTTGA CTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTT
6862 TCCAGCATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
3 19 0.35
4 34 0.62
5 2 0.04
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:6823 original size:25 final size:25
Alignment explanation
Indices: 6789--6837 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
6779 CACCTTATGT
*
6789 TTTATTTTTTACTATTTTTTATTTA
1 TTTATCTTTTACTATTTTTTATTTA
*
6814 TTTATCTTTTATTATTTTTTATTT
1 TTTATCTTTTACTATTTTTTATTT
6838 TTTGACTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTATCTTTTACTATTTTTTATTTA
Found at i:8678 original size:6 final size:6
Alignment explanation
Indices: 8667--8732 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
8657 TGGGCCTAAC
* * * *
8667 AAATTT AAATTT -ATTTT AAAATT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
8713 --ATTAT AAATTT AAATTT AAA
1 AAATT-T AAATTT AAATTT AAA
8733 ATTCATTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 33 0.69
7 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:8696 original size:17 final size:17
Alignment explanation
Indices: 8667--8730 Score: 101
Period size: 17 Copynumber: 3.8 Consensus size: 17
8657 TGGGCCTAAC
8667 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
8684 AAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTT
*
8701 AAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
8718 AAATTTAAATTTA
1 AAATTTAAATTTA
8731 AAATTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:8707 original size:23 final size:24
Alignment explanation
Indices: 8668--8744 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 24
8658 GGGCCTAACA
*
8668 AATT-TAAATTT-ATTTTAAAATT
1 AATTATAAATTTAAATTTAAAATT
*
8690 AAGTT-T-ATTTTAAATTT-AAATT
1 AA-TTATAAATTTAAATTTAAAATT
*
8712 TATTATAAATTTAAATTTAAAATT
1 AATTATAAATTTAAATTTAAAATT
*
8736 CATT-TAAAT
1 AATTATAAAT
8745 AATGTTCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
21 2 0.04
22 13 0.29
23 22 0.49
24 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
AATTATAAATTTAAATTTAAAATT
Found at i:8768 original size:14 final size:14
Alignment explanation
Indices: 8745--8775 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8735 TCATTTAAAT
*
8745 AATGTTCAATACAA
1 AATGTCCAATACAA
8759 AATGTCCAATACAA
1 AATGTCCAATACAA
8773 AAT
1 AAT
8776 TACAAAGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (14 bp):
AATGTCCAATACAA
Found at i:9438 original size:9 final size:9
Alignment explanation
Indices: 9409--9501 Score: 62
Period size: 9 Copynumber: 9.8 Consensus size: 9
9399 TTATCATCAT
*
9409 TATTAATAT
1 TATTAATAA
9418 TATTAATTTAA
1 TATTAA--TAA
9429 TATTAATAA
1 TATTAATAA
**
9438 TGA-CCATAA
1 T-ATTAATAA
*
9447 TAATAATAA
1 TATTAATAA
*
9456 CATTAATAA
1 TATTAATAA
9465 TAATAATAATAA
1 T-AT--TAATAA
*
9477 TACTAATAA
1 TATTAATAA
*
9486 TAATAATAA
1 TATTAATAA
9495 TATTAAT
1 TATTAAT
9502 TAGCATAGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
8 1 0.02
9 46 0.70
10 3 0.05
11 9 0.14
12 7 0.11
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (9 bp):
TATTAATAA
Found at i:9449 original size:3 final size:3
Alignment explanation
Indices: 9443--9501 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
9433 AATAATGACC
* * *
9443 ATA ATA ATA ATA ACA TTA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
9491 ATA ATA TTA AT
1 ATA ATA ATA AT
9502 TAGCATAGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:10681 original size:87 final size:87
Alignment explanation
Indices: 10523--10747 Score: 238
Period size: 87 Copynumber: 2.6 Consensus size: 87
10513 AAGGTTCTCG
* * * ** * * * *
10523 AACTTCCCAAAATCCCATTTTTGACACTTAAACTTCTAAAAAT-TCCATTTTTACCCCTAAATTT
1 AACTTCCAAAAATTCCATTTTT-ACCCTCGAATTTCCAAAAATCT-CATTTTTACCCCCAAACTT
* * *
10587 CCAAAAATCTAATTTTTGACCCCAA
64 CCAAAAATCCAA-TTTTAACCCAAA
* * * *
10612 AACTTTCAAAAATTTCA-TTTTACCCTCGAATTTTCAAAAATCTCATTTTTACCCCCGAACTTCC
1 AACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCTCATTTTTACCCCCAAACTTCC
* *
10676 CAAAATCCCATTTTAACCCAAA
66 AAAAATCCAATTTTAACCCAAA
*
10698 AACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCCCATTTT
1 AACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCTCATTTT
10748 CGACCTCGAA
Statistics
Matches: 112, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
86 25 0.22
87 69 0.62
88 5 0.04
89 13 0.12
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCTCATTTTTACCCCCAAACTTCC
AAAAATCCAATTTTAACCCAAA
Found at i:10757 original size:29 final size:29
Alignment explanation
Indices: 10519--10747 Score: 176
Period size: 29 Copynumber: 7.9 Consensus size: 29
10509 CTTAAAGGTT
* *
10519 CTCGAACTTCCCAAAATCCCATTTTTGACA
1 CTCGAACTTCCAAAAATCCCATTTTT-ACC
** * *
10549 CTTAAACTTCTAAAAATTCCATTTTTACC
1 CTCGAACTTCCAAAAATCCCATTTTTACC
* * **
10578 C-CTAAATTTCCAAAAATCTAATTTTTGACC
1 CTC-GAACTTCCAAAAATCCCATTTTT-ACC
* * **
10608 C-CAAAACTTTCAAAAATTTCA-TTTTACC
1 CTC-GAACTTCCAAAAATCCCATTTTTACC
* * *
10636 CTCGAATTTTCAAAAATCTCATTTTTACC
1 CTCGAACTTCCAAAAATCCCATTTTTACC
* * *
10665 CCCGAACTTCCCAAAATCCCATTTTAACC
1 CTCGAACTTCCAAAAATCCCATTTTTACC
*** *
10694 CAAAAACTTCCAAAAATTCCATTTTTACC
1 CTCGAACTTCCAAAAATCCCATTTTTACC
*
10723 CTCGAATTTCCAAAAATCCCATTTT
1 CTCGAACTTCCAAAAATCCCATTTT
10748 CGACCTCGAA
Statistics
Matches: 158, Mismatches: 37, Indels: 9
0.77 0.18 0.04
Matches are distributed among these distances:
28 19 0.12
29 99 0.63
30 40 0.25
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
CTCGAACTTCCAAAAATCCCATTTTTACC
Found at i:11835 original size:14 final size:14
Alignment explanation
Indices: 11818--11863 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
11808 TGTATATTAA
11818 AATAAAATTTATAT
1 AATAAAATTTATAT
*
11832 AATATCAATTTATAT
1 AATA-AAATTTATAT
* *
11847 ATTAAAATTTTTAT
1 AATAAAATTTATAT
11861 AAT
1 AAT
11864 TAATATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAAAATTTATAT
Found at i:17221 original size:51 final size:53
Alignment explanation
Indices: 17120--17221 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 53
17110 TTTAAATATT
* * * *
17120 AAAAATATATTTTTTGGGTGTTTGTCAACTCATGGTCGACACTCAAAAATAAA
1 AAAAATATATATTTTGGGTGTTTGTCAACTAATGGTCAACACCCAAAAATAAA
* *
17173 AAAAAT-TATATTTT-GGTGTTTGTCATCTAATGG-CTAACACCCACAAATA
1 AAAAATATATATTTTGGGTGTTTGTCAACTAATGGTC-AACACCCAAAAATA
17222 TATTTTTTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
50 1 0.02
51 28 0.67
52 7 0.17
53 6 0.14
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (53 bp):
AAAAATATATATTTTGGGTGTTTGTCAACTAATGGTCAACACCCAAAAATAAA
Found at i:18556 original size:25 final size:25
Alignment explanation
Indices: 18528--18626 Score: 135
Period size: 25 Copynumber: 4.0 Consensus size: 25
18518 TTTTGAATTC
* *
18528 TGGCTCGTAAGAGAGTAATTCTATT
1 TGGCTCGTAAGAGCGTAATTCTGTT
* *
18553 TGGCTCGTAAGAGCGAAATTCTGTC
1 TGGCTCGTAAGAGCGTAATTCTGTT
* *
18578 TGGCTCATAAGCGCGTAATTCTGTT
1 TGGCTCGTAAGAGCGTAATTCTGTT
*
18603 TGGCTCGTAAGAGCGTACTTCTGT
1 TGGCTCGTAAGAGCGTAATTCTGT
18627 CTGGGCTTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (25 bp):
TGGCTCGTAAGAGCGTAATTCTGTT
Found at i:18596 original size:50 final size:50
Alignment explanation
Indices: 18526--18630 Score: 156
Period size: 50 Copynumber: 2.1 Consensus size: 50
18516 AATTTTGAAT
*
18526 TCTGGCTCGTAAGAGAGTAATTCTATTTGGCTCGTAAGAGCGAAATTCTG
1 TCTGGCTCATAAGAGAGTAATTCTATTTGGCTCGTAAGAGCGAAATTCTG
* * * * *
18576 TCTGGCTCATAAGCGCGTAATTCTGTTTGGCTCGTAAGAGCGTACTTCTG
1 TCTGGCTCATAAGAGAGTAATTCTATTTGGCTCGTAAGAGCGAAATTCTG
18626 TCTGG
1 TCTGG
18631 GCTTGTATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (50 bp):
TCTGGCTCATAAGAGAGTAATTCTATTTGGCTCGTAAGAGCGAAATTCTG
Found at i:18642 original size:26 final size:25
Alignment explanation
Indices: 18529--18642 Score: 113
Period size: 25 Copynumber: 4.5 Consensus size: 25
18519 TTTGAATTCT
* * *
18529 GGCTCGTAAGAGAGTAATTCTATTT
1 GGCTCGTAAGAGCGTAATTCTGTTG
*
18554 GGCTCGTAAGAGCGAAATTCTGTCT-
1 GGCTCGTAAGAGCGTAATTCTGT-TG
* * *
18579 GGCTCATAAGCGCGTAATTCTGTTT
1 GGCTCGTAAGAGCGTAATTCTGTTG
*
18604 GGCTCGTAAGAGCGTACTTCTGTCTG
1 GGCTCGTAAGAGCGTAATTCTGT-TG
* *
18630 GGCTTGTATGAGC
1 GGCTCGTAAGAGC
18643 TAAATTTCTG
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
24 1 0.01
25 60 0.81
26 13 0.18
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (25 bp):
GGCTCGTAAGAGCGTAATTCTGTTG
Found at i:19745 original size:31 final size:30
Alignment explanation
Indices: 19702--19762 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
19692 GTACAACCGA
* * *
19702 ATTGCGGGGTTGAATTGTATATTGTCATGT
1 ATTGCGGAGTTGAATTATATACTGTCATGT
19732 ATTGTCGGAGTTGAATTATATACTGTCATGT
1 ATTG-CGGAGTTGAATTATATACTGTCATGT
19763 GAAGCGACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.23, C:0.08, G:0.26, T:0.43
Consensus pattern (30 bp):
ATTGCGGAGTTGAATTATATACTGTCATGT
Found at i:20049 original size:21 final size:21
Alignment explanation
Indices: 20025--20069 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20015 CGAGTTGGCT
20025 AGGAA-TTTCTTGAAGTTGACC
1 AGGAACTTT-TTGAAGTTGACC
* *
20046 AGGAACTTTTTTAAGTTGATC
1 AGGAACTTTTTGAAGTTGACC
20067 AGG
1 AGG
20070 TATTCAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (21 bp):
AGGAACTTTTTGAAGTTGACC
Found at i:20420 original size:61 final size:60
Alignment explanation
Indices: 20332--20494 Score: 181
Period size: 59 Copynumber: 2.8 Consensus size: 60
20322 TTTAATTTTT
* * * *
20332 GGGTGTCGACCATGAGTTGACAAACACCAAAAAAAATATATTTTTGGGTATCT-AGAATAA
1 GGGTATCGATCATGAGTTGACAGACACCAAAAAAAATATATTTTTGGATATCTGAGAA-AA
* *
20392 GGGTTATCGATCATGGGTTGACAGACACC-AAAAAAATAT-TTTTTTGATATCTGAGAAAA
1 GGG-TATCGATCATGAGTTGACAGACACCAAAAAAAATATATTTTTGGATATCTGAGAAAA
* * * * *
20451 GGGTGTCGGTCATGACTTGATAGACATCAAAAAAAATA-ATTTTT
1 GGGTATCGATCATGAGTTGACAGACACCAAAAAAAATATATTTTT
20495 TATTCGTATT
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 19 0.22
59 30 0.34
60 17 0.20
61 21 0.24
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (60 bp):
GGGTATCGATCATGAGTTGACAGACACCAAAAAAAATATATTTTTGGATATCTGAGAAAA
Found at i:20764 original size:21 final size:24
Alignment explanation
Indices: 20740--20792 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
20730 TTACATGAAC
20740 TTTTAAT-A-TTTTTACTAT-T-TA
1 TTTTAATCATTTTTTA-TATATATA
20761 TTTTAAATCATTTTTTATATATATA
1 TTTT-AATCATTTTTTATATATATA
20786 TTTTAAT
1 TTTTAAT
20793 TTAAGCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 4 0.15
22 3 0.11
23 4 0.15
24 10 0.37
25 6 0.22
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTAATCATTTTTTATATATATA
Found at i:22829 original size:36 final size:36
Alignment explanation
Indices: 22778--22848 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
22768 ACTGCATTGC
* **
22778 ACTAAACTATATTATGTGTAAATTTTTTATATATGT
1 ACTAAACTATATTATGTGCAAATAATTTATATATGT
* *
22814 ACTAAATTATTTTATGTGCAAATAATTTATATATG
1 ACTAAACTATATTATGTGCAAATAATTTATATATG
22849 AAAGGTTGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (36 bp):
ACTAAACTATATTATGTGCAAATAATTTATATATGT
Found at i:31921 original size:30 final size:30
Alignment explanation
Indices: 31885--31943 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
31875 ATTAGTAAAA
*
31885 ATAAAATTAT-ATTTTATCTTTTTAAAAATG
1 ATAAAATTATAATTTGAT-TTTTTAAAAATG
*
31915 ATAAAATTTTAATTTGATTTTTTAAAAAT
1 ATAAAATTATAATTTGATTTTTTAAAAAT
31944 TACATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (30 bp):
ATAAAATTATAATTTGATTTTTTAAAAATG
Found at i:33012 original size:24 final size:24
Alignment explanation
Indices: 32980--33028 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
32970 CACGTGATTA
*
32980 TTTCCGTTATTAACTGCAGATGAC
1 TTTCCGTTATTAACCGCAGATGAC
33004 TTTCCGTTATTAACCGCAGATGAC
1 TTTCCGTTATTAACCGCAGATGAC
33028 T
1 T
33029 AAACATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (24 bp):
TTTCCGTTATTAACCGCAGATGAC
Found at i:33993 original size:21 final size:22
Alignment explanation
Indices: 33953--33994 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
33943 TTAGAGTTGC
* *
33953 ATTAATTCATTCTTAGTTTATA
1 ATTAATGCATTCTTAATTTATA
33975 ATTAATGCA-TCTTAATTTAT
1 ATTAATGCATTCTTAATTTAT
33995 TTACTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (22 bp):
ATTAATGCATTCTTAATTTATA
Found at i:34003 original size:10 final size:10
Alignment explanation
Indices: 33990--34028 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
33980 TGCATCTTAA
33990 TTTATTTACT
1 TTTATTTACT
34000 TTTATTTACT
1 TTTATTTACT
*
34010 ATGTTCTTTACT
1 -T-TTATTTACT
34022 TTTATTT
1 TTTATTT
34029 TTTTTTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 15 0.60
11 2 0.08
12 8 0.32
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (10 bp):
TTTATTTACT
Found at i:36570 original size:7 final size:7
Alignment explanation
Indices: 36558--36595 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
36548 TCAATACTGC
36558 CAAAATG
1 CAAAATG
36565 CAAAATG
1 CAAAATG
36572 CAAAATG
1 CAAAATG
36579 C-AAATG
1 CAAAATG
36585 C-AAATG
1 CAAAATG
36591 CAAAA
1 CAAAA
36596 AAAAAAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (7 bp):
CAAAATG
Found at i:36577 original size:14 final size:14
Alignment explanation
Indices: 36558--36595 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
36548 TCAATACTGC
36558 CAAAATGCAAAATG
1 CAAAATGCAAAATG
36572 CAAAATGC-AAATG
1 CAAAATGCAAAATG
36585 C-AAATGCAAAA
1 CAAAATGCAAAA
36596 AAAAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.26
13 9 0.39
14 8 0.35
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (14 bp):
CAAAATGCAAAATG
Found at i:36585 original size:6 final size:6
Alignment explanation
Indices: 36560--36594 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
36550 AATACTGCCA
36560 AAATGC AAAATGC AAAATGC AAATGC AAATGC AAA
1 AAATGC -AAATGC -AAATGC AAATGC AAATGC AAA
36595 AAAAAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 15 0.54
7 13 0.46
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (6 bp):
AAATGC
Found at i:39231 original size:18 final size:18
Alignment explanation
Indices: 39193--39231 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
39183 AAAACAAAAT
*
39193 TTTATATATTTTTATTAA
1 TTTATATATTTTTAATAA
*
39211 TTTATATATTTTTAATGA
1 TTTATATATTTTTAATAA
39229 TTT
1 TTT
39232 TTTAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTATATATTTTTAATAA
Found at i:46560 original size:23 final size:19
Alignment explanation
Indices: 46534--46596 Score: 76
Period size: 18 Copynumber: 3.2 Consensus size: 19
46524 GTTAATAGGG
46534 ACTTTCAATTTATAATTCATATC
1 ACTTTCAATTT-TAATT--T-TC
46557 ACTTTCAATTTTAA-TTTC
1 ACTTTCAATTTTAATTTTC
46575 ACTTTCAATTTTAA-TTTC
1 ACTTTCAATTTTAATTTTC
46593 ACTT
1 ACTT
46597 ATTAAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
18 24 0.60
19 1 0.03
21 1 0.03
22 3 0.08
23 11 0.28
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.52
Consensus pattern (19 bp):
ACTTTCAATTTTAATTTTC
Found at i:46578 original size:18 final size:18
Alignment explanation
Indices: 46555--46596 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
46545 ATAATTCATA
46555 TCACTTTCAATTTTAATT
1 TCACTTTCAATTTTAATT
46573 TCACTTTCAATTTTAATT
1 TCACTTTCAATTTTAATT
46591 TCACTT
1 TCACTT
46597 ATTAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (18 bp):
TCACTTTCAATTTTAATT
Found at i:47423 original size:2 final size:2
Alignment explanation
Indices: 47416--47444 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47406 AAATGTACAA
47416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.