Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002884.1 Kokia drynarioides strain JFW-HI SEQ_115296, 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: 50202
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:3174 original size:30 final size:30
Alignment explanation
Indices: 3133--3220 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 30
3123 TAGTTTTAAT
3133 TTTTATAATTTTTAAAAAATTAAATTAAAA
1 TTTTATAATTTTTAAAAAATTAAATTAAAA
* * * * *
3163 TTTTATCATTTTT-GAATATTAAAATACAA
1 TTTTATAATTTTTAAAAAATTAAATTAAAA
* * *
3192 TTTTATAAATTATAAAAAAACTAAATTAA
1 TTTTAT-AATTTTTAAAAAATTAAATTAA
3221 TATTATACCC
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
29 18 0.42
30 16 0.37
31 9 0.21
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (30 bp):
TTTTATAATTTTTAAAAAATTAAATTAAAA
Found at i:3591 original size:22 final size:23
Alignment explanation
Indices: 3550--3594 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3540 ATTTAGTTTT
3550 TATTTTTATTTTTAACAATTTAA
1 TATTTTTATTTTTAACAATTTAA
*
3573 TATTTTTATTTTTCA-AATTTAA
1 TATTTTTATTTTTAACAATTTAA
3595 AAATATAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTTTATTTTTAACAATTTAA
Found at i:5682 original size:3 final size:3
Alignment explanation
Indices: 5674--5708 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5664 ATGTTTGATG
5674 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5709 GACACGAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:10055 original size:16 final size:15
Alignment explanation
Indices: 10026--10067 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
10016 AAAATCAAAA
10026 TAAAAAATTATTTTT
1 TAAAAAATTATTTTT
*
10041 TAAAAAATCTTTTTTT
1 TAAAAAAT-TATTTTT
*
10057 TAAAATATTAT
1 TAAAAAATTAT
10068 ATCACCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAAAAATTATTTTT
Found at i:12075 original size:3 final size:3
Alignment explanation
Indices: 12063--12111 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
12053 TAATTATAAA
12063 ATT A-T ATT ATT ATT ATT ATT ATT -TAT ATAT ATT A-T ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT ATT ATT ATT ATT
12106 ATT ATT
1 ATT ATT
12112 TTAAACAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 7 0.17
3 29 0.71
4 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12081 original size:9 final size:9
Alignment explanation
Indices: 12063--12111 Score: 52
Period size: 8 Copynumber: 5.7 Consensus size: 9
12053 TAATTATAAA
12063 ATTA-TATT
1 ATTATTATT
12071 ATTATTATT
1 ATTATTATT
12080 ATTATT-TAT
1 ATTATTAT-T
12089 ATATATTA-T
1 AT-TATTATT
12098 ATTATT-TT
1 ATTATTATT
12106 ATTATT
1 ATTATT
12112 TTAAACAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 16 0.44
9 16 0.44
10 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTATTATT
Found at i:14436 original size:24 final size:24
Alignment explanation
Indices: 14400--14475 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 24
14390 AAAAGTATTC
* * *
14400 AATACGCTCACGCTCATCAGCATG
1 AATACGTTTACGCTCACCAGCATG
*
14424 AATACGTTTACGCTCGCCAGCATG
1 AATACGTTTACGCTCACCAGCATG
* **
14448 AATACGTTTACACTTGCCAGCATG
1 AATACGTTTACGCTCACCAGCATG
14472 AATA
1 AATA
14476 TAAGAAACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (24 bp):
AATACGTTTACGCTCACCAGCATG
Found at i:14700 original size:8 final size:8
Alignment explanation
Indices: 14687--14731 Score: 81
Period size: 8 Copynumber: 5.6 Consensus size: 8
14677 AGATAAGATC
14687 AATTACAA
1 AATTACAA
14695 AATTACAA
1 AATTACAA
*
14703 AATTATAA
1 AATTACAA
14711 AATTACAA
1 AATTACAA
14719 AATTACAA
1 AATTACAA
14727 AATTA
1 AATTA
14732 TCTCTAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (8 bp):
AATTACAA
Found at i:14714 original size:24 final size:24
Alignment explanation
Indices: 14687--14732 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
14677 AGATAAGATC
14687 AATTACAAAATTACAAAATTATAA
1 AATTACAAAATTACAAAATTATAA
14711 AATTACAAAATTACAAAATTAT
1 AATTACAAAATTACAAAATTAT
14733 CTCTAACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (24 bp):
AATTACAAAATTACAAAATTATAA
Found at i:21894 original size:17 final size:16
Alignment explanation
Indices: 21872--21914 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
21862 TTTAAATTTT
21872 TTTTTAAAATATATTAA
1 TTTTTAAAAT-TATTAA
* *
21889 TTTTTAATGATTTTTAA
1 TTTTTAA-AATTATTAA
21906 TTTTTAAAA
1 TTTTTAAAA
21915 ATAGTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 19 0.86
18 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTTTAAAATTATTAA
Found at i:21949 original size:16 final size:18
Alignment explanation
Indices: 21920--21953 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
21910 TAAAAATAGT
21920 TTTTATATATATTTTAAA
1 TTTTATATATATTTTAAA
21938 TTTTATA-A-ATTTTAAA
1 TTTTATATATATTTTAAA
21954 AATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATATATATTTTAAA
Found at i:23172 original size:206 final size:205
Alignment explanation
Indices: 22812--23567 Score: 1043
Period size: 206 Copynumber: 3.8 Consensus size: 205
22802 TAGCCACTAT
22812 GTAAATATAAGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGGCACGGGGTT
1 GTAAATATAAGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGGCACGGGGTT
* * * *
22877 CGAT-CCCCGCATCTCCAATGCAATTATATTTAATTTACCTTTTCGTAGTGTCAAAGTTCCTTCA
66 CGATCCCCCGCATCTCCAATGCAATTACACTTAATTTTCCTTTTTGTAGTGTCAAAGTTCCTTCA
22941 AACGGCGTCGTTCACTCTCTCTTGTTCTCCACTTGAGTCTGTACCCGACATTTTATTATGGAAAA
131 AACGGCGTCGTTCACTCTCTCTTGTTCTCCACTTGAGTCTGTACCCGACATTTTATTATGGAAAA
23006 CTTTAAACGTG
196 CTTT-AACGTG
*
23017 GTAAATGTAAGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGGCACGGGGTT
1 GTAAATATAAGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGGCACGGGGTT
* *
23082 CGATCCCCCGCATCTCCACTGCCATTACACTTAATTTTCCTTTTTGTAGTGTCAAAGTTCCTTCA
66 CGATCCCCCGCATCTCCAATGCAATTACACTTAATTTTCCTTTTTGTAGTGTCAAAGTTCCTTCA
* *
23147 AACGGCGTCGTTCACTCTCTCTTGTTCTCCATTTGAGTCTGTACCCAACATTTTATTATGGAAAA
131 AACGGCGTCGTTCACTCTCTCTTGTTCTCCACTTGAGTCTGTACCCGACATTTTATTATGGAAAA
23212 CTTTTAACGTG
196 C-TTTAACGTG
*
23223 GTAAATGTAAGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGGCACGGGGTT
1 GTAAATATAAGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGGCACGGGGTT
* * *
23288 CGATCCCCCGCATCTCCACTGCCATTACACTTATTTTTCCTTTTTGTAGTGTCAAAGTTCCTTCA
66 CGATCCCCCGCATCTCCAATGCAATTACACTTAATTTTCCTTTTTGTAGTGTCAAAGTTCCTTCA
** * * * *
23353 AACGGCGTCGTTCACTCTCTCTT-TT-TCC-C---CCT-TGTA-CGGAAAATTTTATTGT-AAAA
131 AACGGCGTCGTTCACTCTCTCTTGTTCTCCACTTGAGTCTGTACCCG-ACATTTTATTATGGAAA
23409 AC-TT----TG
195 ACTTTAACGTG
** * * *
23415 GCCAGTATATGGGGATGTAGCTCAAATGGTAGAGTGCTCGC-TT--AT--GAGAGGCACGGGGTT
1 GTAAATATAAGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGGCACGGGGTT
* ** * * *
23475 CGATCTCCCGCATCTCCAATGCAATTGTATTTAATTTTCC-TATT-TAGTGGCAAAGTTCCTTCA
66 CGATCCCCCGCATCTCCAATGCAATTACACTTAATTTTCCTTTTTGTAGTGTCAAAGTTCCTTCA
* *
23538 AACGGCGTCGTTCCCTCTCTCTTCTTCTCC
131 AACGGCGTCGTTCACTCTCTCTTGTTCTCC
23568 CCTTTGGTCT
Statistics
Matches: 512, Mismatches: 34, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
185 40 0.08
186 5 0.01
187 51 0.10
189 2 0.00
191 2 0.00
192 37 0.07
196 2 0.00
198 6 0.01
199 14 0.03
200 1 0.00
204 3 0.01
205 70 0.14
206 276 0.54
207 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (205 bp):
GTAAATATAAGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGGCACGGGGTT
CGATCCCCCGCATCTCCAATGCAATTACACTTAATTTTCCTTTTTGTAGTGTCAAAGTTCCTTCA
AACGGCGTCGTTCACTCTCTCTTGTTCTCCACTTGAGTCTGTACCCGACATTTTATTATGGAAAA
CTTTAACGTG
Found at i:27875 original size:22 final size:22
Alignment explanation
Indices: 27828--27877 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
27818 TCTTTTGAAC
* *
27828 TTTAAAGTGTCAACTTTCCTAT
1 TTTAAAGTCTCAACTTTCATAT
*
27850 TTTAAAGTCTCAA-TTTCATGT
1 TTTAAAGTCTCAACTTTCATAT
27871 GTTTAAA
1 -TTTAAA
27878 TACACTCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTAAAGTCTCAACTTTCATAT
Found at i:28442 original size:17 final size:17
Alignment explanation
Indices: 28420--28458 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28410 CTCCACCTTG
* *
28420 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
28437 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
28454 ACAAG
1 ACAAG
28459 TTCTCCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:35945 original size:8 final size:9
Alignment explanation
Indices: 35929--35985 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
35919 ATTAATTAAT
35929 TTTTAAAAA
1 TTTTAAAAA
35938 TTTTAAAAA
1 TTTTAAAAA
*
35947 TTCTAAAAA
1 TTTTAAAAA
*
35956 TTATACAAATTA
1 TTTTA-AAA--A
35968 TTTTTAAAAA
1 -TTTTAAAAA
35978 -TTTAAAAA
1 TTTTAAAAA
35986 GCATAAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
8 8 0.20
9 21 0.51
10 4 0.10
12 4 0.10
13 4 0.10
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:36000 original size:30 final size:31
Alignment explanation
Indices: 35938--36001 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
35928 TTTTTAAAAA
** *
35938 TTTTAAAAATTCTAAAAATTATACAAATTAT
1 TTTTAAAAATTCTAAAAAGCATACAAAATAT
35969 TTTTAAAAATT-TAAAAAGCATA-AGAAATAT
1 TTTTAAAAATTCTAAAAAGCATACA-AAATAT
35999 TTT
1 TTT
36002 AAATTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 17 0.59
31 11 0.38
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (31 bp):
TTTTAAAAATTCTAAAAAGCATACAAAATAT
Found at i:36278 original size:9 final size:9
Alignment explanation
Indices: 36264--36300 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
36254 ATTTAATTAA
36264 TTAAAAATT
1 TTAAAAATT
36273 TTAAAAATT
1 TTAAAAATT
*
36282 TTAAATATT
1 TTAAAAATT
*
36291 TTAAATATT
1 TTAAAAATT
36300 T
1 T
36301 ATTACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTAAAAATT
Found at i:44986 original size:19 final size:17
Alignment explanation
Indices: 44952--44986 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
44942 ATAAAGTATT
44952 AATAAAATTAACAATAA
1 AATAAAATTAACAATAA
44969 AATAAAAGTTATACAATA
1 AATAAAA-TTA-ACAATA
44987 CTCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (17 bp):
AATAAAATTAACAATAA
Found at i:47938 original size:12 final size:12
Alignment explanation
Indices: 47921--47945 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47911 ATGTTATAAC
47921 ATAAATATTGTT
1 ATAAATATTGTT
47933 ATAAATATTGTT
1 ATAAATATTGTT
47945 A
1 A
47946 ATAGCCTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Done.