Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009526.1 Kokia drynarioides strain JFW-HI SEQ_124238, 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: 21492
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:2672 original size:29 final size:28
Alignment explanation
Indices: 2640--2700 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
2630 AAAATGAGAC
*
2640 TTTTCGGATGCCCGGGGGCAAAATGGTAA
1 TTTT-GGATGCCCGGGGGAAAAATGGTAA
* * *
2669 TTTTGGATTCTCGGGGTAAAAATGGTAA
1 TTTTGGATGCCCGGGGGAAAAATGGTAA
2697 TTTT
1 TTTT
2701 ATGAAAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (28 bp):
TTTTGGATGCCCGGGGGAAAAATGGTAA
Found at i:2751 original size:30 final size:30
Alignment explanation
Indices: 2681--2850 Score: 96
Period size: 30 Copynumber: 5.7 Consensus size: 30
2671 TTGGATTCTC
2681 GGGGTAAAAATGGTAA-TTTTATGAAAATTCGG
1 GGGGTAAAAATGG-AATTTTTA-G-AAATTCGG
** * *
2713 GGTTTAAAAATAGAATTTTTAGACATTCGG
1 GGGGTAAAAATGGAATTTTTAGAAATTCGG
* * **
2743 GGGGT-AAAAGGGTATTTTTGAGAGTTTC-G
1 GGGGTAAAAATGGAATTTTT-AGAAATTCGG
* * **
2772 GGGGTAAAAATGGAATTTTTGGAAGTTTTG
1 GGGGTAAAAATGGAATTTTTAGAAATTCGG
* * * * *
2802 AGGTTAAAAATGGGATTTTTGGAAGTTC-G
1 GGGGTAAAAATGGAATTTTTAGAAATTCGG
* * *
2831 AGGTTAAAAATGGGATTTTT
1 GGGGTAAAAATGGAATTTTT
2851 GGAAGTTTTG
Statistics
Matches: 113, Mismatches: 21, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
29 42 0.37
30 53 0.47
31 3 0.03
32 15 0.13
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (30 bp):
GGGGTAAAAATGGAATTTTTAGAAATTCGG
Found at i:2833 original size:29 final size:29
Alignment explanation
Indices: 2776--2857 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
2766 GTTTCGGGGG
* *
2776 TAAAAATGGAATTTTTGGAAGTTTTGAGGT
1 TAAAAATGGGATTTTTGGAAG-TTCGAGGT
2806 TAAAAATGGGATTTTTGGAAGTTCGAGGT
1 TAAAAATGGGATTTTTGGAAGTTCGAGGT
2835 TAAAAATGGGATTTTTGGAAGTT
1 TAAAAATGGGATTTTTGGAAGTT
2858 TTGGGACCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 30 0.60
30 20 0.40
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTCGAGGT
Found at i:3983 original size:3 final size:3
Alignment explanation
Indices: 3938--3971 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
3928 CTTTTCCTTT
*
3938 TTA TTA TTA TTAA TAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
3972 AAACATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:4720 original size:17 final size:17
Alignment explanation
Indices: 4695--4784 Score: 74
Period size: 17 Copynumber: 5.1 Consensus size: 17
4685 GGACTTTTAA
* **
4695 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
4712 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
4729 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAA-TAAAT
*
4746 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
*
4765 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
4783 TT
1 TT
4785 GAATCAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
16 5 0.08
17 27 0.44
18 10 0.16
19 18 0.30
20 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:4724 original size:6 final size:6
Alignment explanation
Indices: 4710--4775 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
4700 TTTTAAATCC
* **
4710 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
**
4757 AGATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
4776 AATAAATTTG
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
5 7 0.15
6 36 0.77
7 4 0.09
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:5555 original size:206 final size:204
Alignment explanation
Indices: 5244--5739 Score: 686
Period size: 206 Copynumber: 2.4 Consensus size: 204
5234 ACTTTCCCGT
* * ** *
5244 ATCAGGACGCTATTCCGTTTTATTATTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGT
1 ATCAGGAAGCTA-ACCGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT--GGT
* * * * *
5309 TCGAAGGTTTGCCCACACCGAGCATGGGCTTGACTTGGTCTTCTTCTCGGTATCTCATCAAGAAG
63 TTGAAGATTTGCTCACATCGAGCATGGGCTTGACTTGGTCTTCTTCTCAGTATCTCATCAAGAAG
* * * * *
5374 ATGACTGCGTTGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACT
128 ATGACCGCATTGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGATTCACT
*
5439 TCTTAGTATCTC
193 TCTCAGTATCTC
* **
5451 ATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCAATATCTGGTCAGGAAGCTAGGATT
1 ATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GG-TT
* * * * *
5516 TGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTTTTCTCAGTATCTCATCAGGAAGA
64 TGAAGATTTGCTCACATCGAGCATGGGCTTGACTTGGTCTTCTTCTCAGTATCTCATCAAGAAGA
5581 TGACCGCATTGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGATTCACTT
129 TGACCGCATTGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGATTCACTT
5646 CTCAGTATCTC
194 CTCAGTATCTC
* *
5657 ATCAAGAAGCTAACCGTTTTATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGTGTT
1 ATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGT-TT
*
5722 CGAAGATTTGCTCGCATC
65 -GAAGATTTGCTCACATC
5740 AAGTCCTGAG
Statistics
Matches: 255, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
204 1 0.00
205 6 0.02
206 237 0.93
207 11 0.04
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.35
Consensus pattern (204 bp):
ATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGTTTG
AAGATTTGCTCACATCGAGCATGGGCTTGACTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATG
ACCGCATTGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGATTCACTTCT
CAGTATCTC
Found at i:6157 original size:123 final size:122
Alignment explanation
Indices: 5643--6139 Score: 519
Period size: 115 Copynumber: 4.2 Consensus size: 122
5633 ATTTGATTCA
* * * * *
5643 CTTCTCAGTATCTCATCAAGAAGCTAACCGTTTTATTGCTTCGACTTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATTGTTTCGACCTGCCTCTCAGTATCTCGTC
* ** * * *
5708 AGGAAGCT-GGTGTTCGAAGATTTGCTCGCATCAAG--TC----C--TGAGTTGGTATA
66 AGGAAGCTAGG-GTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTGA-TTTGTCTT
* *
5758 CTTCTCTGTATCTCATCAGGAAGCCAA-C-TTTTATTGTTTCGACCTGCCTCTCAGTATCTCGTC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATTGTTTCGACCTGCCTCTCAGTATCTCGTC
*
5821 AGGAAGCTAAGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTGATTTGGTCTT
66 AGGAAGCTAGGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTGATTT-GTCTT
* * ** * * *
5879 CTTCTCAGTATCTCATTATGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTTAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATTGTTTCGACCTGCCTCTCAGTATCTCGTC
* * * * * *
5944 AAGAAGCT-GGTGTTCGAAGATTTGCTCGCATCGAG--TC-TTT-A--G-TTCGTATA
66 AGGAAGCTAGG-GTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTGATTTGTCTT
* ** *
5994 CTTCTCTGTATCTCATCAGGAAGCTAACTATTTTATTGTTTTGACCTGCCTCTCAGTATCTCGTC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATTGTTTCGACCTGCCTCTCAGTATCTCGTC
* *
6059 AGGAAGCTAGGGCTCGGAGATTTGCTCGCTTTGAGCCTCGTTTCATTGATTTGATCTT
66 AGGAAGCTAGGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTGATTTG-TCTT
6117 CTTCTCAGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
6140 GTGACCGCAT
Statistics
Matches: 310, Mismatches: 50, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
113 60 0.19
114 2 0.01
115 110 0.35
116 4 0.01
117 3 0.01
118 3 0.01
119 3 0.01
120 5 0.02
121 32 0.10
122 5 0.02
123 83 0.27
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (122 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATTGTTTCGACCTGCCTCTCAGTATCTCGTC
AGGAAGCTAGGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTGATTTGTCTT
Found at i:6382 original size:28 final size:28
Alignment explanation
Indices: 6342--6399 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
6332 ACTTATATGA
6342 ATGTGTATGATGAATGTCAGATTTATTT
1 ATGTGTATGATGAATGTCAGATTTATTT
6370 ATGTGTATGATGAATGTCAGATTTATTT
1 ATGTGTATGATGAATGTCAGATTTATTT
6398 AT
1 AT
6400 TATTCAGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (28 bp):
ATGTGTATGATGAATGTCAGATTTATTT
Found at i:17882 original size:20 final size:21
Alignment explanation
Indices: 17859--17906 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
17849 ATTTTGTGAG
17859 TTTTGAGGG-TAAAAATGGAAT
1 TTTTG-GGGTTAAAAATGGAAT
*
17880 TTTTGGGGTTAAAAATGGGAT
1 TTTTGGGGTTAAAAATGGAAT
17901 TTTTGG
1 TTTTGG
17907 AAGTTCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (21 bp):
TTTTGGGGTTAAAAATGGAAT
Found at i:17908 original size:30 final size:29
Alignment explanation
Indices: 17874--17968 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
17864 AGGGTAAAAA
*
17874 TGGAATTTTTGGGGTTAAAAATGGGATTTT
1 TGGAA-TTTTGGGGTTAAAAATGGAATTTT
* *
17904 TGGAAGTTCGAGGG-TAAAAATGGAATTTT
1 TGGAATTTTG-GGGTTAAAAATGGAATTTT
**
17933 TAAAAGTTTTGGGGTTAAAAATGGAATTTTT
1 TGGAA-TTTTGGGGTTAAAAATGGAA-TTTT
17964 TGGAA
1 TGGAA
17969 GTTTAGGGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
29 23 0.44
30 22 0.42
31 7 0.13
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (29 bp):
TGGAATTTTGGGGTTAAAAATGGAATTTT
Found at i:17922 original size:29 final size:29
Alignment explanation
Indices: 17884--17971 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
17874 TGGAATTTTT
*
17884 GGGGTTAAAAATGGGATTTTTGGAAGTTC
1 GGGGTTAAAAATGGAATTTTTGGAAGTTC
** *
17913 GAGGG-TAAAAATGGAATTTTTAAAAGTTTT
1 G-GGGTTAAAAATGGAATTTTTGGAAG-TTC
17943 GGGGTTAAAAATGGAATTTTTTGGAAGTT
1 GGGGTTAAAAATGGAA-TTTTTGGAAGTT
17972 TAGGGACCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 22 0.45
30 19 0.39
31 8 0.16
ACGTcount: A:0.33, C:0.01, G:0.30, T:0.36
Consensus pattern (29 bp):
GGGGTTAAAAATGGAATTTTTGGAAGTTC
Found at i:19071 original size:3 final size:3
Alignment explanation
Indices: 19027--19059 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
19017 TTATTAACGC
19027 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA
19060 AAACATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:19809 original size:17 final size:17
Alignment explanation
Indices: 19784--19891 Score: 78
Period size: 17 Copynumber: 6.3 Consensus size: 17
19774 GGACTTTTAA
* **
19784 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
19801 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
19818 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAA-TAAAT
*
19835 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
*
19854 TTAAATTTAAAATTAAA-
1 TTAAATTTTAAA-TAAAT
* *
19871 ATAAA-TTTGAATAAAT
1 TTAAATTTTAAATAAAT
19887 TTAAA
1 TTAAA
19892 CCCAATAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
15 4 0.05
16 13 0.18
17 32 0.44
18 9 0.12
19 14 0.19
20 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:19813 original size:6 final size:6
Alignment explanation
Indices: 19799--19891 Score: 70
Period size: 6 Copynumber: 16.2 Consensus size: 6
19789 TTTTAAATCC
* **
19799 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
** * * *
19846 AGATAA ATTTAA ATTTAA AATTAA A-ATAA ATTTGA A--TAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
19891 A
1 A
19892 CCCAATAAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
4 3 0.05
5 11 0.17
6 48 0.73
7 4 0.06
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:19817 original size:11 final size:11
Alignment explanation
Indices: 19801--19891 Score: 60
Period size: 11 Copynumber: 8.0 Consensus size: 11
19791 TTAAATCCAT
*
19801 TTAAATTTTAA
1 TTAAATTTAAA
19812 TTAAATTTAAA
1 TTAAATTTAAA
**
19823 TTTAAA-GCAAA
1 -TTAAATTTAAA
19834 TTTAAATTTAAAA
1 -TTAAATTT-AAA
*
19847 GATAAATTTAAA
1 -TTAAATTTAAA
*
19859 TTTAAAATTAAA
1 -TTAAATTTAAA
* *
19871 ATAAATTTGAA
1 TTAAATTTAAA
19882 -TAAATTTAAA
1 TTAAATTTAAA
19892 CCCAATAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
10 9 0.14
11 27 0.43
12 17 0.27
13 10 0.16
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:19855 original size:19 final size:18
Alignment explanation
Indices: 19799--19891 Score: 88
Period size: 17 Copynumber: 5.4 Consensus size: 18
19789 TTTTAAATCC
* *
19799 ATTTAAATTT-TAATTAA
1 ATTTAAATTTAAAAGTAA
*
19816 ATTTAAATTT-AAAGCAA
1 ATTTAAATTTAAAAGTAA
19833 ATTTAAATTTAAAAGATAA
1 ATTTAAATTTAAAAG-TAA
*
19852 ATTTAAATTTAAAATTAA
1 ATTTAAATTTAAAAGTAA
* *
19870 A-ATAAATTT-GAA-TAA
1 ATTTAAATTTAAAAGTAA
19885 ATTTAAA
1 ATTTAAA
19892 CCCAATAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
15 4 0.06
16 6 0.09
17 31 0.48
18 8 0.12
19 16 0.25
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTTAAATTTAAAAGTAA
Done.