Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007454.1 Kokia drynarioides strain JFW-HI SEQ_122075, 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: 113404
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1829 original size:25 final size:25
Alignment explanation
Indices: 1801--1853 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1791 CAAGAAAAGA
* * *
1801 TTGATGTTCTAGACTTGTTGATGCT
1 TTGATCTTCTAGACATGATGATGCT
1826 TTGATCTTCTAGACATGATGATGCT
1 TTGATCTTCTAGACATGATGATGCT
1851 TTG
1 TTG
1854 TGAACATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (25 bp):
TTGATCTTCTAGACATGATGATGCT
Found at i:11356 original size:22 final size:22
Alignment explanation
Indices: 11329--11376 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
11319 TGTCATTTTA
*
11329 TGGCAACCAAAGGCATTTTTCT
1 TGGCAACAAAAGGCATTTTTCT
11351 TGGCAACAAAAGGCATTTTTCT
1 TGGCAACAAAAGGCATTTTTCT
11373 TGGC
1 TGGC
11377 CATCGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (22 bp):
TGGCAACAAAAGGCATTTTTCT
Found at i:15587 original size:17 final size:17
Alignment explanation
Indices: 15565--15600 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15555 TTTTCCCTAG
*
15565 TTGTCATTACATTTTAA
1 TTGTCACTACATTTTAA
*
15582 TTGTCACTGCATTTTAA
1 TTGTCACTACATTTTAA
15599 TT
1 TT
15601 ATTCTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (17 bp):
TTGTCACTACATTTTAA
Found at i:34222 original size:2 final size:2
Alignment explanation
Indices: 34202--34286 Score: 138
Period size: 2 Copynumber: 43.5 Consensus size: 2
34192 CAACATTTAT
*
34202 TA TA TA -A TA -A TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
34242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34284 TA T
1 TA T
34287 TTCTCTTTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
1 2 0.03
2 75 0.97
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:34315 original size:21 final size:22
Alignment explanation
Indices: 34290--34337 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
34280 TATATATTTC
*
34290 TCTTTTTTTTA-TCAATTTTTT
1 TCTTTTCTTTATTCAATTTTTT
**
34311 TC-TTTCTTTATTCCTTTTTTT
1 TCTTTTCTTTATTCAATTTTTT
34332 TCTTTT
1 TCTTTT
34338 ATGTGATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.32
21 12 0.55
22 3 0.14
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (22 bp):
TCTTTTCTTTATTCAATTTTTT
Found at i:35349 original size:3 final size:3
Alignment explanation
Indices: 35328--35382 Score: 51
Period size: 3 Copynumber: 18.0 Consensus size: 3
35318 GGGCAATATT
* *
35328 TTC TTC TTT TTC TTCC TTC TTC TTC TT- TTC TTTC TTC TTC ATT- TCC
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC -TTC TTC TTC -TTC TTC
35374 TTC TTC TTC
1 TTC TTC TTC
35383 CTCTACCGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 3 0.07
3 32 0.74
4 8 0.19
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:35358 original size:18 final size:19
Alignment explanation
Indices: 35328--35367 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
35318 GGGCAATATT
35328 TTCTTCTTTTTCTTCCTTC
1 TTCTTCTTTTTCTTCCTTC
*
35347 TTCTTC-TTTTCTTTCTTC
1 TTCTTCTTTTTCTTCCTTC
35365 TTC
1 TTC
35368 ATTTCCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTCTTCTTTTTCTTCCTTC
Found at i:35364 original size:15 final size:15
Alignment explanation
Indices: 35328--35382 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
35318 GGGCAATATT
*
35328 TTCTTCTTTTTCTTCC
1 TTCTTCTTCTT-TTCC
*
35344 TTCTTCTTCTTTTCT
1 TTCTTCTTCTTTTCC
*
35359 TTCTTCTTCATTTCC
1 TTCTTCTTCTTTTCC
35374 TTCTTCTTC
1 TTCTTCTTC
35383 CTCTACCGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
15 25 0.71
16 10 0.29
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCTTCTTCTTTTCC
Found at i:57238 original size:6 final size:6
Alignment explanation
Indices: 57227--57285 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
57217 CAAGTACTCT
* * *
57227 ACAAAA ATAAAA GACAAAA ACAAAA GCAAAA ATAAAAA ACAAAA ACAAATA
1 ACAAAA ACAAAA -ACAAAA ACAAAA ACAAAA A-CAAAA ACAAAA ACAAA-A
57278 ACCAAAA A
1 A-CAAAA A
57286 TTTCTATGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
6 25 0.58
7 14 0.33
8 4 0.09
ACGTcount: A:0.78, C:0.14, G:0.03, T:0.05
Consensus pattern (6 bp):
ACAAAA
Found at i:57245 original size:13 final size:13
Alignment explanation
Indices: 57227--57271 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
57217 CAAGTACTCT
57227 ACAAAAATAAAAG
1 ACAAAAATAAAAG
*
57240 ACAAAAACAAAAG
1 ACAAAAATAAAAG
*
57253 -CAAAAATAAAAA
1 ACAAAAATAAAAG
57265 ACAAAAA
1 ACAAAAA
57272 CAAATAACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.80, C:0.11, G:0.04, T:0.04
Consensus pattern (13 bp):
ACAAAAATAAAAG
Found at i:57262 original size:25 final size:25
Alignment explanation
Indices: 57228--57275 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
57218 AAGTACTCTA
*
57228 CAAAAATAAAAGACAAAAACAAAAG
1 CAAAAATAAAAAACAAAAACAAAAG
57253 CAAAAATAAAAAACAAAAACAAA
1 CAAAAATAAAAAACAAAAACAAA
57276 TAACCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.79, C:0.12, G:0.04, T:0.04
Consensus pattern (25 bp):
CAAAAATAAAAAACAAAAACAAAAG
Found at i:59079 original size:18 final size:18
Alignment explanation
Indices: 59056--59100 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
59046 GCTTGTCCTC
59056 AAGCAAACAAAACAAGAA
1 AAGCAAACAAAACAAGAA
* *
59074 AAGCAAAGAAAGCAAGAA
1 AAGCAAACAAAACAAGAA
*
59092 AAGAAAACA
1 AAGCAAACA
59101 TAGGAGCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.71, C:0.13, G:0.16, T:0.00
Consensus pattern (18 bp):
AAGCAAACAAAACAAGAA
Found at i:61564 original size:5 final size:5
Alignment explanation
Indices: 61554--61578 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
61544 TATAGATACA
61554 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
61579 TCGTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:70541 original size:36 final size:36
Alignment explanation
Indices: 70476--70579 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
70466 TGATCGTTAT
* *
70476 TCATTTTATTCCCTATTGACCCTG-AGGTCATGATGC
1 TCATTTTACTCCCTGTTGACCC-GAAGGTCATGATGC
* * * *
70512 TCATTTTAGTCTCTGTTGATCCGATGGTCATGATGC
1 TCATTTTACTCCCTGTTGACCCGAAGGTCATGATGC
70548 TCATTTTACTCCCTGTTGACCCGAAGGTCATG
1 TCATTTTACTCCCTGTTGACCCGAAGGTCATG
70580 CCTATTACCA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 1 0.02
36 57 0.98
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.38
Consensus pattern (36 bp):
TCATTTTACTCCCTGTTGACCCGAAGGTCATGATGC
Found at i:76982 original size:12 final size:12
Alignment explanation
Indices: 76965--76993 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
76955 GCAACTAACT
76965 ACTAAAAAGTAA
1 ACTAAAAAGTAA
76977 ACTAAAAAGTAA
1 ACTAAAAAGTAA
76989 ACTAA
1 ACTAA
76994 CTCAATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.10, G:0.07, T:0.17
Consensus pattern (12 bp):
ACTAAAAAGTAA
Found at i:77360 original size:3 final size:3
Alignment explanation
Indices: 77352--77406 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
77342 GGGAAACTTT
*
77352 TTC TTC TTC TTC TTCC TTC -TC TTC TT- TTCC TTC CTC TTC TCTC TT-
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TT-C TTC TTC TTC T-TC TTC
77397 TTC TTC TTC T
1 TTC TTC TTC T
77407 GTTTCAATAC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
2 6 0.14
3 30 0.68
4 8 0.18
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:77376 original size:15 final size:16
Alignment explanation
Indices: 77356--77396 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
77346 AACTTTTTCT
77356 TCTTCTTCTTCCTT-C
1 TCTTCTTCTTCCTTCC
77371 TCTTCTT-TTCCTTCC
1 TCTTCTTCTTCCTTCC
77386 TCTTCTCTCTT
1 TCTTCT-TCTT
77397 TTCTTCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.26
15 14 0.61
16 1 0.04
17 2 0.09
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
TCTTCTTCTTCCTTCC
Found at i:77379 original size:27 final size:27
Alignment explanation
Indices: 77348--77404 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
77338 GTCGGGGAAA
* *
77348 CTTTTTCTTCTTCTTCT-TCCTTCTCTT
1 CTTTTCCTTCCTCTTCTCT-CTTCTCTT
*
77375 CTTTTCCTTCCTCTTCTCTCTTTTCTT
1 CTTTTCCTTCCTCTTCTCTCTTCTCTT
77402 CTT
1 CTT
77405 CTGTTTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (27 bp):
CTTTTCCTTCCTCTTCTCTCTTCTCTT
Found at i:81226 original size:14 final size:14
Alignment explanation
Indices: 81178--81220 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
81168 TGAACATATA
81178 ATAAATAAATAAAT
1 ATAAATAAATAAAT
81192 CAATAGAA-AAATAAAT
1 --ATA-AATAAATAAAT
81208 ATAAATAAATAAA
1 ATAAATAAATAAA
81221 AGTAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
16 11 0.44
17 2 0.08
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (14 bp):
ATAAATAAATAAAT
Found at i:81227 original size:26 final size:26
Alignment explanation
Indices: 81182--81233 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
81172 CATATAATAA
* *
81182 ATAAATAAATCAATAGAAAAATAAAT
1 ATAAATAAATCAAAAGAAAAAAAAAT
81208 ATAAATAAAT-AAAAGTAAAAAAAAAT
1 ATAAATAAATCAAAAG-AAAAAAAAAT
81234 TGGGTTGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (26 bp):
ATAAATAAATCAAAAGAAAAAAAAAT
Found at i:88443 original size:16 final size:17
Alignment explanation
Indices: 88422--88457 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
88412 TAGCAATATA
*
88422 TTTCTTTTCTTCTT-TT
1 TTTCTTTTCCTCTTCTT
88438 TTTCTTTTCCTCTTCTT
1 TTTCTTTTCCTCTTCTT
88455 TTT
1 TTT
88458 TTTAAGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTTCCTCTTCTT
Found at i:89036 original size:17 final size:18
Alignment explanation
Indices: 89016--89057 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
89006 ACTACAATGT
89016 AAATGCACTAACAAAT-A
1 AAATGCACTAACAAATAA
* *
89033 AAATGCAGTGACAAATAA
1 AAATGCACTAACAAATAA
89051 AAATGCA
1 AAATGCA
89058 ATGACAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.17
Consensus pattern (18 bp):
AAATGCACTAACAAATAA
Found at i:89055 original size:18 final size:18
Alignment explanation
Indices: 89016--89069 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
89006 ACTACAATGT
* *
89016 AAATGCACTAACAAAT-A
1 AAATGCAATGACAAATAA
*
89033 AAATGCAGTGACAAATAA
1 AAATGCAATGACAAATAA
*
89051 AAATGCAATGACAACTAA
1 AAATGCAATGACAAATAA
89069 A
1 A
89070 TAAAATGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (18 bp):
AAATGCAATGACAAATAA
Found at i:89076 original size:21 final size:19
Alignment explanation
Indices: 89028--89078 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
89018 ATGCACTAAC
*
89028 AAATAAAATGCAGTGACAA
1 AAATAAAATGCAATGACAA
*
89047 ATA-AAAATGCAATGACAA
1 AAATAAAATGCAATGACAA
89065 CTAAATAAAATGCA
1 --AAATAAAATGCA
89079 TGTAACTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 14 0.54
19 2 0.08
20 2 0.08
21 8 0.31
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (19 bp):
AAATAAAATGCAATGACAA
Found at i:109640 original size:18 final size:17
Alignment explanation
Indices: 109610--109677 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
109600 GCATGCACAT
*
109610 CATGATCAAATGCAACCA
1 CATGCTCAAATGCAA-CA
* *
109628 CATGCTCAGATGCAGTCA
1 CATGCTCAAATGCA-ACA
*
109646 CATGCTTAAATGCAGACA
1 CATGCTCAAATGCA-ACA
*
109664 CATGCTCGAATGCA
1 CATGCTCAAATGCA
109678 GCCATAACAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (17 bp):
CATGCTCAAATGCAACA
Done.