Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003069.1 Kokia drynarioides strain JFW-HI SEQ_115609, 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: 88321
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7334 original size:91 final size:92
Alignment explanation
Indices: 7194--7366 Score: 217
Period size: 91 Copynumber: 1.9 Consensus size: 92
7184 TAACATTAGG
* * * *
7194 TACCATAATAAAATACAAATTGGTAGTTTAGGTATCACATTGTATATTTTCAAAA-TACAGGTAC
1 TACCATAATAAAACACAAATTGATAGTTTAGGTATCACATTGGACATTTT-AAAAGTACAGGTAC
7258 CACATTGGAAATTTTATGGAAGTATAGA
65 CACATTGGAAATTTTATGGAAGTATAGA
** * *
7286 TACCATAATAAAACAC-GTTTGATAGTTTAGGTA-CTACATTGGACATTTTAAAAGTGCAGGTAT
1 TACCATAATAAAACACAAATTGATAGTTTAGGTATC-ACATTGGACATTTTAAAAGTACAGGTAC
* *
7349 CACGTTGGACATTTTATG
65 CACATTGGAAATTTTATG
7367 AAAATACAAG
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
90 5 0.07
91 49 0.71
92 15 0.22
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (92 bp):
TACCATAATAAAACACAAATTGATAGTTTAGGTATCACATTGGACATTTTAAAAGTACAGGTACC
ACATTGGAAATTTTATGGAAGTATAGA
Found at i:9499 original size:3 final size:3
Alignment explanation
Indices: 9491--9516 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9481 GAAAAAGACA
9491 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
9517 CGTGTCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12066 original size:13 final size:13
Alignment explanation
Indices: 12048--12073 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12038 TATATTTTTA
12048 TTATTTGATATTT
1 TTATTTGATATTT
12061 TTATTTGATATTT
1 TTATTTGATATTT
12074 AATAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (13 bp):
TTATTTGATATTT
Found at i:14788 original size:23 final size:23
Alignment explanation
Indices: 14760--14816 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
14750 TAACGTGGCA
14760 TCCAGTCAGCAGCTTCTAAAAGG
1 TCCAGTCAGCAGCTTCTAAAAGG
*
14783 TCCAGTCAGCAGCTTCTAGAAGG
1 TCCAGTCAGCAGCTTCTAAAAGG
14806 TCCAGTCAGCA
1 TCCAGTCAGCA
14817 ATGATGGACG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (23 bp):
TCCAGTCAGCAGCTTCTAAAAGG
Found at i:17746 original size:23 final size:24
Alignment explanation
Indices: 17720--17768 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
17710 ACAATCAATC
* *
17720 CATTTTCTATTA-ATTTACTCTGA
1 CATTTTATATTACATTTACACTGA
*
17743 CATTTTATATTACATTTGCACTGA
1 CATTTTATATTACATTTACACTGA
17767 CA
1 CA
17769 AGATTTAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (24 bp):
CATTTTATATTACATTTACACTGA
Found at i:19699 original size:55 final size:55
Alignment explanation
Indices: 19634--19744 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
19624 ACTGTGGCGA
19634 TAATATAATTGGTTCTTTAGGGGAAAACCAAGAAGAGGTTCCTCTAAAATACCCT
1 TAATATAATTGGTTCTTTAGGGGAAAACCAAGAAGAGGTTCCTCTAAAATACCCT
19689 TAATATAATTGGTTCTTTAGGGGAAAACCAAGAAGAGGTTCCTCTAAAATACCCT
1 TAATATAATTGGTTCTTTAGGGGAAAACCAAGAAGAGGTTCCTCTAAAATACCCT
19744 T
1 T
19745 TCCCTTGCTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (55 bp):
TAATATAATTGGTTCTTTAGGGGAAAACCAAGAAGAGGTTCCTCTAAAATACCCT
Found at i:21551 original size:20 final size:20
Alignment explanation
Indices: 21526--21565 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21516 AGGCTATGGA
21526 AGGTTGAAGAACCACTCTTT
1 AGGTTGAAGAACCACTCTTT
21546 AGGTTGAAGAACCACTCTTT
1 AGGTTGAAGAACCACTCTTT
21566 CTCAAGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (20 bp):
AGGTTGAAGAACCACTCTTT
Found at i:24229 original size:18 final size:18
Alignment explanation
Indices: 24208--24242 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
24198 CCACATGATC
24208 TTCCTCAGGATCTTCTTT
1 TTCCTCAGGATCTTCTTT
24226 TTCCTCAGGATCTTCTT
1 TTCCTCAGGATCTTCTT
24243 CTTCTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.29, G:0.11, T:0.49
Consensus pattern (18 bp):
TTCCTCAGGATCTTCTTT
Found at i:25031 original size:116 final size:114
Alignment explanation
Indices: 24891--25139 Score: 338
Period size: 116 Copynumber: 2.2 Consensus size: 114
24881 CTACCCTGCA
* * * * * *
24891 ACTTCTATCGATACAAGTATTTAAACTATTAATACCTTAATGTACTGAACTACCGATACCTGTTA
1 ACTTCTA-CGATACAAGCATTTAAACTATCAATACCTCAATGTACAGAACAACCGATACCTATTA
*
24956 TACAACTACCAAAACAACTCAAGTCAGAGAACAACCTCTCTCCTACCTTGT
65 TACAACTACC-AAACAACTCAAGTCAGAGAACAACCTCTCTCCTACCATGT
* * * * *
25007 ACTTTTACTGATACAAGCATTTAAATTATCGATACCTCAATGTACAGAACAATCGATGCCTATTA
1 ACTTCTAC-GATACAAGCATTTAAACTATCAATACCTCAATGTACAGAACAACCGATACCTATTA
*
25072 TACAACTACCGAACAACTCAAGTCAGAGAACAACCTCTCTCCTACCATGT
65 TACAACTACCAAACAACTCAAGTCAGAGAACAACCTCTCTCCTACCATGT
*
25122 GCTTCTAC-ATACAAGCAT
1 ACTTCTACGATACAAGCAT
25140 GAGTTCTACC
Statistics
Matches: 117, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
113 10 0.09
115 45 0.38
116 62 0.53
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (114 bp):
ACTTCTACGATACAAGCATTTAAACTATCAATACCTCAATGTACAGAACAACCGATACCTATTAT
ACAACTACCAAACAACTCAAGTCAGAGAACAACCTCTCTCCTACCATGT
Found at i:26713 original size:32 final size:32
Alignment explanation
Indices: 26676--26741 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
26666 AAATTAGAAG
26676 ATAAAATTTTTACTACCTTTTGTTGAAATTAA
1 ATAAAATTTTTACTACCTTTTGTTGAAATTAA
**
26708 ATAAAATTTTTACTATTTTTTGTTGAAATTAA
1 ATAAAATTTTTACTACCTTTTGTTGAAATTAA
26740 AT
1 AT
26742 CCAAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (32 bp):
ATAAAATTTTTACTACCTTTTGTTGAAATTAA
Found at i:43766 original size:20 final size:19
Alignment explanation
Indices: 43736--43847 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 19
43726 TGGCCTGTAT
*
43736 GCACTTCGGTGCCCTTGTTA
1 GCACTT-GGTGCCCCTGTTA
43756 GCACTCTGGTGCCCCTG-TA
1 GCACT-TGGTGCCCCTGTTA
43775 TGCACTTCGGTGCCCCTGTTA
1 -GCACTT-GGTGCCCCTGTTA
* *
43796 GCATTTTGGTGCCCCT-ATA
1 GCA-CTTGGTGCCCCTGTTA
*
43815 TGCACTTCGATGCCCCT-TTA
1 -GCACTT-GGTGCCCCTGTTA
43835 -CACTTTGGTGCCC
1 GCAC-TTGGTGCCC
43848 TTGAAAATAA
Statistics
Matches: 77, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.12
19 9 0.12
20 54 0.70
21 5 0.06
ACGTcount: A:0.12, C:0.33, G:0.22, T:0.33
Consensus pattern (19 bp):
GCACTTGGTGCCCCTGTTA
Found at i:43784 original size:40 final size:40
Alignment explanation
Indices: 43729--43847 Score: 179
Period size: 40 Copynumber: 3.0 Consensus size: 40
43719 TGAGTTATGG
* *
43729 CCTGTATGCACTTCGGTGCCCTTGTTAGCACTCTGGTGCC
1 CCTGTATGCACTTCGGTGCCCCTGTTAGCACTTTGGTGCC
*
43769 CCTGTATGCACTTCGGTGCCCCTGTTAGCATTTTGGTGCC
1 CCTGTATGCACTTCGGTGCCCCTGTTAGCACTTTGGTGCC
* *
43809 CCTATATGCACTTCGATGCCCCT-TTA-CACTTTGGTGCC
1 CCTGTATGCACTTCGGTGCCCCTGTTAGCACTTTGGTGCC
43847 C
1 C
43848 TTGAAAATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
38 12 0.16
39 3 0.04
40 58 0.79
ACGTcount: A:0.12, C:0.33, G:0.22, T:0.34
Consensus pattern (40 bp):
CCTGTATGCACTTCGGTGCCCCTGTTAGCACTTTGGTGCC
Found at i:44259 original size:19 final size:21
Alignment explanation
Indices: 44235--44280 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
44225 AATAAAGAAA
*
44235 TTTTAGA-AG-TTTGGATGTG
1 TTTTAGAGAGTTTTGAATGTG
44254 TTTTAGAGAGTTTTGAATGTG
1 TTTTAGAGAGTTTTGAATGTG
*
44275 ATTTAG
1 TTTTAG
44281 TTATAGGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 14 0.61
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (21 bp):
TTTTAGAGAGTTTTGAATGTG
Found at i:47317 original size:23 final size:23
Alignment explanation
Indices: 47274--47317 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
47264 AAACTATATA
*
47274 AATAAATATTAAAAAATAAAAAT
1 AATAAATATTAAAAAAAAAAAAT
*
47297 AATAAAT-TTAAAATAAAAAAA
1 AATAAATATTAAAAAAAAAAAA
47318 CTAACCTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (23 bp):
AATAAATATTAAAAAAAAAAAAT
Found at i:51379 original size:21 final size:21
Alignment explanation
Indices: 51349--51388 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51339 TGGGCTTGCG
*
51349 GGAGATAAAGG-ATTTGATTGA
1 GGAGACAAAGGTA-TTGATTGA
51370 GGAGACAAAGGTATTGATT
1 GGAGACAAAGGTATTGATT
51389 TACGTAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.38, C:0.03, G:0.33, T:0.28
Consensus pattern (21 bp):
GGAGACAAAGGTATTGATTGA
Found at i:65551 original size:21 final size:23
Alignment explanation
Indices: 65527--65568 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
65517 AATAATAAAA
*
65527 TATTATT-ATTTAT-TATATTAT
1 TATTATTCATTAATATATATTAT
65548 TATTATTCATTAATATATATT
1 TATTATTCATTAATATATATT
65569 TTGATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATTCATTAATATATATTAT
Found at i:67489 original size:20 final size:22
Alignment explanation
Indices: 67450--67489 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
67440 TATAAAACTA
*
67450 TTAAAATTATTAAAATTATTTT
1 TTAAAATTATTAAAACTATTTT
67472 TTAAAA-TA-TAAAACTATT
1 TTAAAATTATTAAAACTATT
67490 ATATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAAATTATTAAAACTATTTT
Found at i:70149 original size:21 final size:19
Alignment explanation
Indices: 70123--70175 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 19
70113 GGAGTTTTTG
70123 GTATCGGTAGATGCATGACTT
1 GTATCGGTAGAT-CAT-ACTT
70144 GTATCGGTAGAAATCATACTT
1 GTATCGGTAG--ATCATACTT
70165 GTATCGGTAGA
1 GTATCGGTAGA
70176 GCTAGCACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
21 24 0.80
22 3 0.10
23 2 0.07
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.32
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:71765 original size:3 final size:3
Alignment explanation
Indices: 71757--71785 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
71747 GATCATATTT
71757 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
71786 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:71934 original size:19 final size:19
Alignment explanation
Indices: 71910--71947 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
71900 CTTCGTCAAT
71910 TAGTTTTATACTTTTTAAC
1 TAGTTTTATACTTTTTAAC
71929 TAGTTTTATACTTTTTAAC
1 TAGTTTTATACTTTTTAAC
71948 GCTGTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (19 bp):
TAGTTTTATACTTTTTAAC
Found at i:72117 original size:13 final size:12
Alignment explanation
Indices: 72085--72122 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
72075 TTCTCATTCC
*
72085 CCTTTCCCTTTT
1 CCTTTCCATTTT
72097 CCTTTCCATTTT
1 CCTTTCCATTTT
72109 CCATTTCCATTTT
1 CC-TTTCCATTTT
72122 C
1 C
72123 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.08, C:0.37, G:0.00, T:0.55
Consensus pattern (12 bp):
CCTTTCCATTTT
Found at i:73286 original size:3 final size:3
Alignment explanation
Indices: 73280--73310 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
73270 CTTAAGTACC
73280 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
73311 TGATTAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:77498 original size:17 final size:19
Alignment explanation
Indices: 77461--77498 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
77451 TATAATTCTT
77461 ATTCAAACAATATTATTTTA
1 ATTCAAAC-ATATTATTTTA
77481 ATTCAAAC-TATT-TTTTA
1 ATTCAAACATATTATTTTA
77498 A
1 A
77499 GGAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
20 8 0.44
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTCAAACATATTATTTTA
Found at i:78825 original size:6 final size:6
Alignment explanation
Indices: 78814--78844 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
78804 TGAAGATACT
78814 GATTTG GATTTG GATTTG GATTTG GATTTG G
1 GATTTG GATTTG GATTTG GATTTG GATTTG G
78845 TTATGGCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.48
Consensus pattern (6 bp):
GATTTG
Found at i:86948 original size:19 final size:17
Alignment explanation
Indices: 86918--86967 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
86908 ATTAAAATGG
*
86918 TAAAAAATTATAAATAA
1 TAAAAAAATATAAATAA
*
86935 TTATTAAAAATATAAATAA
1 -TA-AAAAAATATAAATAA
86954 TAAAAAAATATAAA
1 TAAAAAAATATAAA
86968 ATCCTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 11 0.39
18 4 0.14
19 13 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAAAAATATAAATAA
Found at i:86963 original size:8 final size:9
Alignment explanation
Indices: 86918--86968 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
86908 ATTAAAATGG
86918 TAAAAAATTA
1 TAAAAAA-TA
*
86928 TAAATAATTA
1 TAAA-AAATA
*
86938 TTAAAAATA
1 TAAAAAATA
*
86947 TAAATAATA
1 TAAAAAATA
86956 -AAAAAATA
1 TAAAAAATA
86964 TAAAA
1 TAAAA
86969 TCCTTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
8 7 0.21
9 15 0.45
10 9 0.27
11 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
TAAAAAATA
Found at i:87560 original size:22 final size:22
Alignment explanation
Indices: 87509--87561 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
87499 TTTTTTTTTA
* *
87509 GATTTTTCAAATAATTATTTAT
1 GATTTTTTAAATAATTAGTTAT
*
87531 -ATAATTTTAAATAATTAGTTAT
1 GAT-TTTTTAAATAATTAGTTAT
87553 GATTTTTTA
1 GATTTTTTA
87562 TATTTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (22 bp):
GATTTTTTAAATAATTAGTTAT
Done.