Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015159.1 Kokia drynarioides strain JFW-HI SEQ_130203, 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: 71723
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 176 characters in sequence are not A, C, G, or T
Found at i:5777 original size:11 final size:11
Alignment explanation
Indices: 5754--5788 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5744 AGGTGAATTA
5754 CCTTTCCTTTT
1 CCTTTCCTTTT
5765 CC-TTCCTTATT
1 CCTTTCCTT-TT
5776 CCTTTCCTTTT
1 CCTTTCCTTTT
5787 CC
1 CC
5789 ACGTATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.27
11 10 0.45
12 6 0.27
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (11 bp):
CCTTTCCTTTT
Found at i:24518 original size:21 final size:21
Alignment explanation
Indices: 24477--24539 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 21
24467 TATTGTGAAA
* *
24477 AAAAATAAATATT-ATATTAAT
1 AAAAAT-AATTTTAATACTAAT
24498 AAAAATAATTTTAATACTAAT
1 AAAAATAATTTTAATACTAAT
24519 AAATTAATATATATTTAATAC
1 AAA--AATA-AT-TTTAATAC
24540 ATAAAATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 5 0.14
21 16 0.46
23 4 0.11
24 2 0.06
25 8 0.23
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATAATTTTAATACTAAT
Found at i:37670 original size:9 final size:9
Alignment explanation
Indices: 37650--37856 Score: 88
Period size: 9 Copynumber: 22.2 Consensus size: 9
37640 TGATACAAAA
37650 ATAAAAAGTT
1 ATAAAAA-TT
37660 ATAAAAATT
1 ATAAAAATT
37669 ATAAAAATT
1 ATAAAAATT
**
37678 ATTAAATTTT
1 A-TAAAAATT
37688 AATAAAAATAT
1 -ATAAAAAT-T
* **
37699 TTAAATTTT
1 ATAAAAATT
*
37708 ATTAAAATT
1 ATAAAAATT
*
37717 A-GAAAA--
1 ATAAAAATT
37723 A-AAAAATT
1 ATAAAAATT
37731 ATAAAAATCGT
1 ATAAAAAT--T
*
37742 AAAAAAAATT
1 -ATAAAAATT
*
37752 ATAAAAAAT
1 ATAAAAATT
*
37761 ATAAAAGTAT
1 ATAAAAAT-T
*
37771 AGAAAAATT
1 ATAAAAATT
*
37780 ATAAAACTT
1 ATAAAAATT
*
37789 -TATAAAATCA
1 ATA-AAAAT-T
*
37799 AAAGAAAATT
1 ATA-AAAATT
37809 ATAAAAATGT
1 ATAAAAAT-T
37819 A-AAGAAA-T
1 ATAA-AAATT
37827 AT-AAAATT
1 ATAAAAATT
*
37835 CGTAAAAAATT
1 -AT-AAAAATT
37846 ATAAAAATT
1 ATAAAAATT
37855 AT
1 AT
37857 TGTACCAAAA
Statistics
Matches: 147, Mismatches: 30, Indels: 41
0.67 0.14 0.19
Matches are distributed among these distances:
6 5 0.03
7 3 0.02
8 11 0.07
9 67 0.46
10 39 0.27
11 15 0.10
12 7 0.05
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:37672 original size:19 final size:18
Alignment explanation
Indices: 37650--37856 Score: 88
Period size: 19 Copynumber: 11.1 Consensus size: 18
37640 TGATACAAAA
37650 ATAAAAAGTTATAAAAATT
1 ATAAAAA-TTATAAAAATT
**
37669 ATAAAAATTATTAAATTTT
1 ATAAAAATTA-TAAAAATT
* **
37688 AATAAAAATATTTAAATTTT
1 -ATAAAAAT-TATAAAAATT
* *
37708 ATTAAAATTA-GAAAA--
1 ATAAAAATTATAAAAATT
37723 A-AAAAATTATAAAAATCGT
1 ATAAAAATTATAAAAAT--T
* *
37742 AAAAAAAATTATAAAAAAT
1 -ATAAAAATTATAAAAATT
* *
37761 ATAAAAGTATAGAAAAATT
1 ATAAAAAT-TATAAAAATT
* *
37780 ATAAAACTT-TATAAAATCA
1 ATAAAAATTATA-AAAAT-T
*
37799 AAAGAAAATTATAAAAATGT
1 ATA-AAAATTATAAAAAT-T
37819 A-AAGAAA-TAT-AAAATT
1 ATAA-AAATTATAAAAATT
*
37835 CGTAAAAAATTATAAAAATT
1 -AT-AAAAATTATAAAAATT
37855 AT
1 AT
37857 TGTACCAAAA
Statistics
Matches: 143, Mismatches: 24, Indels: 42
0.68 0.11 0.20
Matches are distributed among these distances:
14 7 0.05
15 5 0.03
16 1 0.01
17 8 0.06
18 23 0.16
19 48 0.34
20 34 0.24
21 17 0.12
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (18 bp):
ATAAAAATTATAAAAATT
Found at i:37692 original size:20 final size:20
Alignment explanation
Indices: 37669--37714 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
37659 TATAAAAATT
37669 ATAAAAAT-TATTAAATTTTA
1 ATAAAAATAT-TTAAATTTTA
37689 ATAAAAATATTTAAATTTTA
1 ATAAAAATATTTAAATTTTA
*
37709 TTAAAA
1 ATAAAA
37715 TTAGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAAAAATATTTAAATTTTA
Found at i:37765 original size:21 final size:21
Alignment explanation
Indices: 37721--37766 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
37711 AAAATTAGAA
*
37721 AAAAAAAATTATAAAAATCGT
1 AAAAAAAATTATAAAAATCAT
37742 AAAAAAAATTATAAAAAAT-AT
1 AAAAAAAATTAT-AAAAATCAT
37763 AAAA
1 AAAA
37767 GTATAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAAAAAATTATAAAAATCAT
Found at i:38038 original size:21 final size:21
Alignment explanation
Indices: 38013--38057 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
38003 TTAAAAGACC
*
38013 TTTTTATGCA-TTTTATAATAT
1 TTTTTATG-ATTTTTATAAAAT
38034 TTTTTATGATTTTTATAAAAT
1 TTTTTATGATTTTTATAAAAT
38055 TTT
1 TTT
38058 ACATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTATGATTTTTATAAAAT
Found at i:38045 original size:20 final size:20
Alignment explanation
Indices: 38013--38079 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
38003 TTAAAAGACC
38013 TTTTTATGCATTTTATAATAT
1 TTTTTATG-ATTTTATAATAT
*
38034 TTTTTATGATTTTTATAAAAT
1 TTTTTATGA-TTTTATAATAT
** **
38055 TTTACATTTTTTTATAAT-T
1 TTTTTATGATTTTATAATAT
38074 TTTTTA
1 TTTTTA
38080 CAATTTTAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.14
20 9 0.24
21 23 0.62
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTTATGATTTTATAATAT
Found at i:38065 original size:29 final size:27
Alignment explanation
Indices: 38028--38161 Score: 81
Period size: 29 Copynumber: 4.5 Consensus size: 27
38018 ATGCATTTTA
**
38028 TAATATTTTTTATGATTTTTATAAAATTT
1 TAAT-TTTTTTATATTTTT-ATAAAATTT
* *
38057 TACATTTTTTTATAATTTTTTTACAATTT
1 TA-ATTTTTTTAT-ATTTTTATAAAATTT
*
38086 TAATTTTTTT-TTTCTAATTTATAATAAGTTT
1 TAATTTTTTTATAT-T--TTTATAA-AA-TTT
*
38117 TAAATATTTTTATATTTTTATTAAAATTT
1 T-AATTTTTTTATATTTTTA-TAAAATTT
*
38146 AATAATTTTTATATAT
1 --TAATTTTTTTATAT
38162 CTTATTGATT
Statistics
Matches: 82, Mismatches: 11, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
26 1 0.01
27 2 0.02
28 8 0.10
29 27 0.33
30 25 0.30
31 8 0.10
32 9 0.11
33 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (27 bp):
TAATTTTTTTATATTTTTATAAAATTT
Found at i:38104 original size:20 final size:20
Alignment explanation
Indices: 38072--38110 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
38062 TTTTTTATAA
38072 TTTTTTTACAATTT-TAATT
1 TTTTTTTACAATTTATAATT
*
38091 TTTTTTTTCTAATTTATAAT
1 TTTTTTTAC-AATTTATAAT
38111 AAGTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTTTACAATTTATAATT
Found at i:39353 original size:60 final size:59
Alignment explanation
Indices: 39260--39377 Score: 209
Period size: 60 Copynumber: 2.0 Consensus size: 59
39250 GTTGGCATTT
39260 TGATTGATCCGAAGAGTCTAGCTCCCTCACATCTGTTCTTTTACTAATGATGTGTTCTTC
1 TGATTGATCCGAAGAGTCTAGCTCCCTCACATCTGTTC-TTTACTAATGATGTGTTCTTC
* *
39320 TGATTGATCCGAAGAGTTTGGCTCCCTCACATCTGTTCTTTACTAATGATGTGTTCTT
1 TGATTGATCCGAAGAGTCTAGCTCCCTCACATCTGTTCTTTACTAATGATGTGTTCTT
39378 ACTTGTTGGG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 20 0.36
60 36 0.64
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (59 bp):
TGATTGATCCGAAGAGTCTAGCTCCCTCACATCTGTTCTTTACTAATGATGTGTTCTTC
Found at i:52210 original size:20 final size:20
Alignment explanation
Indices: 52185--52239 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
52175 CAAATGCTCT
*
52185 TTTGAATCGATTCATTATTG
1 TTTGAATCGATTCATTATTA
**
52205 TTTGAATCGATTGTTTATTA
1 TTTGAATCGATTCATTATTA
52225 TTTGAATCGATTCAT
1 TTTGAATCGATTCAT
52240 CTTGGTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (20 bp):
TTTGAATCGATTCATTATTA
Found at i:59642 original size:2 final size:2
Alignment explanation
Indices: 59635--59667 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
59625 TTACTTACTT
*
59635 TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
59668 TAATTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:62148 original size:8 final size:8
Alignment explanation
Indices: 62135--62165 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
62125 CTTTAATGGT
62135 AAAAAAAG
1 AAAAAAAG
62143 AAAAAAAG
1 AAAAAAAG
62151 AAAAAAAG
1 AAAAAAAG
62159 AAAAAAA
1 AAAAAAA
62166 AACGAGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:70560 original size:20 final size:21
Alignment explanation
Indices: 70537--70583 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
70527 TAGTTGTTCT
70537 GGTAGAAA-CATACTTGTATC
1 GGTAGAAACCATACTTGTATC
*
70557 GGTA-AAACCATAGTTGTATC
1 GGTAGAAACCATACTTGTATC
*
70577 AGTAGAA
1 GGTAGAA
70584 GAGGAGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 18 0.78
21 2 0.09
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (21 bp):
GGTAGAAACCATACTTGTATC
Done.