Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011632.1 Kokia drynarioides strain JFW-HI SEQ_126623, 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: 16308
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:7698 original size:44 final size:41
Alignment explanation
Indices: 7648--7770 Score: 115
Period size: 44 Copynumber: 3.0 Consensus size: 41
7638 ATTATATTAT
*
7648 TGTTTTGGTGTTGTTTTTTTGCTATTTTCGTTGCTATTTTTTAC
1 TGTTTTGGTGTTGTTTTTTTGCTATTTT--TTGAT-TTTTTTAC
* * * *
7692 TGTTTTGGTATTGTGTTTTTACTA--TTTTGATTTTTTTAT
1 TGTTTTGGTGTTGTTTTTTTGCTATTTTTTGATTTTTTTAC
** * *
7731 TGTTTTGGTTGTTGTTTTGGTGCTATTTTTTCATTATTTT
1 TGTTTTGG-TGTTGTTTTTTTGCTATTTTTTGATTTTTTT
7771 GGTGTTGTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
39 15 0.23
40 15 0.23
42 13 0.20
44 21 0.33
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.67
Consensus pattern (41 bp):
TGTTTTGGTGTTGTTTTTTTGCTATTTTTTGATTTTTTTAC
Found at i:7805 original size:24 final size:24
Alignment explanation
Indices: 7778--7846 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
7768 TTTGGTGTTG
7778 TTTTTATTGTTATTTTTGTTGCTA
1 TTTTTATTGTTATTTTTGTTGCTA
* *
7802 TTTTT-TCTATTATTTTTGTTGCTG
1 TTTTTAT-TGTTATTTTTGTTGCTA
* *
7826 TTTTGATTGTTATTTTGGTTG
1 TTTTTATTGTTATTTTTGTTG
7847 TCTTGATGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.70
Consensus pattern (24 bp):
TTTTTATTGTTATTTTTGTTGCTA
Found at i:7836 original size:48 final size:46
Alignment explanation
Indices: 7731--7846 Score: 144
Period size: 48 Copynumber: 2.5 Consensus size: 46
7721 ATTTTTTTAT
* * * *
7731 TGTTTTGGTTGTT-GTTTTGGTGCTATTTTTTCATTATTTTGGTGT
1 TGTTTTGATTGTTATTTTTGTTGCTATTTTTTCATTATTTTGGTGC
* *
7776 TGTTTTTATTGTTATTTTTGTTGCTATTTTTTCTATTATTTTTGTTGC
1 TGTTTTGATTGTTATTTTTGTTGCTATTTTTTC-ATTA-TTTTGGTGC
*
7824 TGTTTTGATTGTTATTTTGGTTG
1 TGTTTTGATTGTTATTTTTGTTG
7847 TCTTGATGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 11 0.18
46 17 0.28
47 4 0.07
48 28 0.47
ACGTcount: A:0.09, C:0.04, G:0.20, T:0.67
Consensus pattern (46 bp):
TGTTTTGATTGTTATTTTTGTTGCTATTTTTTCATTATTTTGGTGC
Found at i:9374 original size:19 final size:19
Alignment explanation
Indices: 9328--9374 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
9318 GATTTGTGTT
9328 TTCTACACTATCAATGTTTAA
1 TTCTACACTATCAATG--TAA
*
9349 GTCTACACTATCAATG-AA
1 TTCTACACTATCAATGTAA
9367 CTTCTACA
1 -TTCTACA
9375 TTGAAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 6 0.26
21 15 0.65
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.36
Consensus pattern (19 bp):
TTCTACACTATCAATGTAA
Found at i:10334 original size:27 final size:28
Alignment explanation
Indices: 10283--10339 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
10273 AATAAGTTTA
* **
10283 AATATACTATGAAAAAATATTTAAATAT
1 AATATAATATGAAAAAATAAATAAATAT
10311 AATATAATATG-AAAAATAAATAAATAT
1 AATATAATATGAAAAAATAAATAAATAT
10338 AA
1 AA
10340 AATCTCAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (28 bp):
AATATAATATGAAAAAATAAATAAATAT
Found at i:10336 original size:17 final size:18
Alignment explanation
Indices: 10305--10341 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
10295 AAAAATATTT
10305 AAATATAATATAATATGAA
1 AAATATAATATAATAT-AA
10324 AAATA-AATA-AATATAA
1 AAATATAATATAATATAA
10340 AA
1 AA
10342 TCTCAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 5 0.28
18 4 0.22
19 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (18 bp):
AAATATAATATAATATAA
Found at i:15108 original size:17 final size:17
Alignment explanation
Indices: 15053--15145 Score: 87
Period size: 17 Copynumber: 5.4 Consensus size: 17
15043 CTAAACTCCT
*
15053 TTTAATTTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
15070 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
*
15088 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
15105 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* **
15123 TTTAAAATTATCATAAA
1 TTTAAATTTATTTTAAA
15140 TTTAAA
1 TTTAAA
15146 ATAAATAAAG
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
17 34 0.55
18 28 0.45
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:15110 original size:35 final size:35
Alignment explanation
Indices: 15053--15147 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 35
15043 CTAAACTCCT
* * *
15053 TTTAATTTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAATTAAAATTATTTAAAAA
** **
15088 TTTAAATTTATTTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAATTAAAATTATTTAAAAA
* ** *
15123 TTTAAAATTATCATAAATTTAAAAT
1 TTTAAATTTATTTTAAAATTAAAAT
15148 AAATAAAGCC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (35 bp):
TTTAAATTTATTTTAAAATTAAAATTATTTAAAAA
Found at i:15796 original size:138 final size:138
Alignment explanation
Indices: 15548--15826 Score: 549
Period size: 138 Copynumber: 2.0 Consensus size: 138
15538 CCATATGAGA
15548 AACCTATAGAAGGGGGGAGATTTTCTGTAATACGTTAAAAAAAAATACAAAATTTTCTTTGGCAA
1 AACCTATAGAAGGGGGGAGATTTTCTGTAATACGTTAAAAAAAAATACAAAATTTTCTTTGGCAA
15613 TCAAATAGAGAACATTCCAAAATTAATTGAAAAACGATTGCGCACAGATATATAAGCCAGAAGTA
66 TCAAATAGAGAACATTCCAAAATTAATTGAAAAACGATTGCGCACAGATATATAAGCCAGAAGTA
15678 TTCGAGGT
131 TTCGAGGT
*
15686 AACCTGTAGAAGGGGGGAGATTTTCTGTAATACGTTAAAAAAAAATACAAAATTTTCTTTGGCAA
1 AACCTATAGAAGGGGGGAGATTTTCTGTAATACGTTAAAAAAAAATACAAAATTTTCTTTGGCAA
15751 TCAAATAGAGAACATTCCAAAATTAATTGAAAAACGATTGCGCACAGATATATAAGCCAGAAGTA
66 TCAAATAGAGAACATTCCAAAATTAATTGAAAAACGATTGCGCACAGATATATAAGCCAGAAGTA
15816 TTCGAGGT
131 TTCGAGGT
15824 AAC
1 AAC
15827 AGACTCGATC
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 140 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (138 bp):
AACCTATAGAAGGGGGGAGATTTTCTGTAATACGTTAAAAAAAAATACAAAATTTTCTTTGGCAA
TCAAATAGAGAACATTCCAAAATTAATTGAAAAACGATTGCGCACAGATATATAAGCCAGAAGTA
TTCGAGGT
Found at i:16134 original size:12 final size:12
Alignment explanation
Indices: 16119--16181 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
16109 ATAACCCCAT
16119 TAATAATATTAA
1 TAATAATATTAA
** *
16131 TAATTGTTTTAA
1 TAATAATATTAA
* *
16143 TGATAATAATAA
1 TAATAATATTAA
*
16155 TAATAATAATAA
1 TAATAATATTAA
*
16167 TAATAATTTTAA
1 TAATAATATTAA
16179 TAA
1 TAA
16182 AAAAAAAATC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:16151 original size:3 final size:3
Alignment explanation
Indices: 16140--16173 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
16130 ATAATTGTTT
*
16140 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
16174 TTTAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Done.