Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002692.1 Kokia drynarioides strain JFW-HI SEQ_114966, 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: 27119
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:624 original size:21 final size:22
Alignment explanation
Indices: 598--642 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
588 TACTTAAATT
598 TTTTTTATAA-AA-TAATGAATA
1 TTTTTTA-AAGAAGTAATGAATA
619 TTTTTTAAAGAAGTAATGAATA
1 TTTTTTAAAGAAGTAATGAATA
641 TT
1 TT
643 AATGTAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.09
21 9 0.41
22 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (22 bp):
TTTTTTAAAGAAGTAATGAATA
Found at i:787 original size:23 final size:22
Alignment explanation
Indices: 761--831 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
751 TTTTTTTAGT
761 TTTTATTTGTCTTTGTGGCACGA
1 TTTT-TTTGTCTTTGTGGCACGA
* * *
784 TTTTTCTGTC-TTGTGACACGC
1 TTTTTTTGTCTTTGTGGCACGA
*
805 TTTTCCTTT-ACTTTGTGGCACG-
1 TTTT--TTTGTCTTTGTGGCACGA
827 TTTTT
1 TTTTT
832 GCCTTATGGC
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 13 0.33
22 10 0.26
23 15 0.38
ACGTcount: A:0.10, C:0.18, G:0.18, T:0.54
Consensus pattern (22 bp):
TTTTTTTGTCTTTGTGGCACGA
Found at i:803 original size:21 final size:22
Alignment explanation
Indices: 768--831 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
758 AGTTTTTATT
*
768 TGTCTTTGTGGCACGATTTTTC
1 TGTCTTTGTGACACGATTTTTC
* *
790 TGTC-TTGTGACACGCTTTTCC
1 TGTCTTTGTGACACGATTTTTC
* *
811 TTTACTTTGTGGCACG-TTTTT
1 TGT-CTTTGTGACACGATTTTT
832 GCCTTATGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 16 0.47
22 9 0.26
23 9 0.26
ACGTcount: A:0.09, C:0.20, G:0.20, T:0.50
Consensus pattern (22 bp):
TGTCTTTGTGACACGATTTTTC
Found at i:1223 original size:13 final size:13
Alignment explanation
Indices: 1207--1243 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1197 CTTTTATATG
1207 AAATATTTAAATA
1 AAATATTTAAATA
*
1220 AAATAATTAAAATA
1 AAAT-ATTTAAATA
1234 AAATATTTAA
1 AAATATTTAA
1244 TGATTCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATATTTAAATA
Found at i:2122 original size:2 final size:2
Alignment explanation
Indices: 2115--2143 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2105 TTTTATATCG
2115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2144 TGTTAGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3859 original size:29 final size:29
Alignment explanation
Indices: 3826--3884 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3816 TTTTCGGGTC
3826 TTAATTTGTAACATTTAAAAGCTTTAAAA
1 TTAATTTGTAACATTTAAAAGCTTTAAAA
3855 TTAATTTGTAACATTTAAAAGCTTTAAAA
1 TTAATTTGTAACATTTAAAAGCTTTAAAA
3884 T
1 T
3885 ACGATCCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (29 bp):
TTAATTTGTAACATTTAAAAGCTTTAAAA
Found at i:4561 original size:30 final size:30
Alignment explanation
Indices: 4526--4850 Score: 155
Period size: 29 Copynumber: 10.9 Consensus size: 30
4516 GTGAAATAGT
* *
4526 AATTTTGGGAAAATTCGGGGTTAAAAATGA
1 AATTTTTGGAAATTTCGGGGTTAAAAATGA
* * *
4556 AATTTTTAGACA-TTCGGGAG-TAAAAATGG
1 AATTTTTGGAAATTTCGGG-GTTAAAAATGA
* * * *
4585 AATTTTTTGAAGTTTCGGGGGTCAAAAATGG
1 AATTTTTGGAAATTTC-GGGGTTAAAAATGA
* * * *
4616 GATTTTGGGAAGTTT-GAGGGTAAAAAAATGA
1 AATTTTTGGAAATTTCG-GGGT-TAAAAATGA
* ** *
4647 AATTTTTGGAATTTTAAGGGTCAAAAATGA
1 AATTTTTGGAAATTTCGGGGTTAAAAATGA
* * *
4677 AATTTTTGGAAGTTTTGGGGTT-AAAATGG
1 AATTTTTGGAAATTTCGGGGTTAAAAATGA
* * * *
4706 GATTTTGGGAAGTTT-GAGGG-TAAAAATGG
1 AATTTTTGGAAATTTCG-GGGTTAAAAATGA
* *** * *
4735 AATTTTTGGAAGTTTTAAGGTCAAAATTTG-
1 AATTTTTGGAAATTTCGGGGTTAAAA-ATGA
* * *
4765 AATTTTTAGAAGTTTTGGGGTTAAAAAT-A
1 AATTTTTGGAAATTTCGGGGTTAAAAATGA
* * * *
4794 AGA-TTTTGGGAAGTTCGGGGGTAAAAATGG
1 A-ATTTTTGGAAATTTCGGGGTTAAAAATGA
* * * *
4824 AATTTTTGTAAGTTTCGAGGTCAAAAA
1 AATTTTTGGAAATTTCGGGGTTAAAAA
4851 ATGGGATTTT
Statistics
Matches: 229, Mismatches: 50, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
28 2 0.01
29 90 0.39
30 89 0.39
31 48 0.21
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAATTTCGGGGTTAAAAATGA
Found at i:4640 original size:29 final size:30
Alignment explanation
Indices: 4577--4873 Score: 248
Period size: 30 Copynumber: 9.9 Consensus size: 30
4567 ATTCGGGAGT
* *
4577 AAAAATGGAATTTTTTGAAGTTTCGGGGGTC
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGTC
* * *
4608 AAAAATGGGATTTTGGGAAGTTTGAGGGTAA
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT-C
* * *
4639 AAAAATGAAATTTTTGGAATTTTAAGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTC
*
4669 AAAAATGAAATTTTTGGAAGTTTTG-GGGT-
1 AAAAATGGAATTTTTGGAAG-TTTGAGGGTC
* * *
4698 TAAAATGGGATTTTGGGAAGTTTGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTC
* *
4727 AAAAATGGAATTTTTGGAAGTTTTAAGGTC
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTC
* * * *
4757 AAAATTTGAATTTTTAGAAGTTTTG-GGGTT
1 AAAAATGGAATTTTTGGAAG-TTTGAGGGTC
* * * *
4787 AAAAAT-AAGATTTTGGGAAGTTCGGGGGT-
1 AAAAATGGA-ATTTTTGGAAGTTTGAGGGTC
*
4816 AAAAATGGAATTTTTGTAAGTTTCGA-GGTC
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGTC
* * *
4846 AAAAAATGGGATTTTGGGAAGTTCGAGG
1 -AAAAATGGAATTTTTGGAAGTTTGAGG
4874 ACCTTCAGGG
Statistics
Matches: 212, Mismatches: 42, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
28 4 0.02
29 68 0.32
30 70 0.33
31 70 0.33
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGGTC
Found at i:4816 original size:89 final size:88
Alignment explanation
Indices: 4577--4850 Score: 354
Period size: 89 Copynumber: 3.1 Consensus size: 88
4567 ATTCGGGAGT
* * *
4577 AAAAATGGAATTTTTTGAAGTTTCGGGGGTCAAAAATGGGATTTTGGGAAGTTTGAGGGTAAAAA
1 AAAAAT-GAATTTTTAGAAGTTT-TGGGGTTAAAAATGGGATTTTGGGAAGTTTGAGGGT--AAA
*
4642 AATGAAATTTTTGGAA-TTTTAAGGGTC
62 AATGGAATTTTTGGAAGTTTTAA-GGTC
*
4669 AAAAATGAAATTTTTGGAAGTTTTGGGGTT-AAAATGGGATTTTGGGAAGTTTGAGGGTAAAAAT
1 AAAAATG-AATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTGGGAAGTTTGAGGGTAAAAAT
4733 GGAATTTTTGGAAGTTTTAAGGTC
65 GGAATTTTTGGAAGTTTTAAGGTC
* ** * *
4757 AAAATTTGAATTTTTAGAAGTTTTGGGGTTAAAAATAAGATTTTGGGAAGTTCGGGGGTAAAAAT
1 AAAA-ATGAATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTGGGAAGTTTGAGGGTAAAAAT
* **
4822 GGAATTTTTGTAAGTTTCGAGGTC
65 GGAATTTTTGGAAGTTTTAAGGTC
4846 AAAAA
1 AAAAA
4851 ATGGGATTTT
Statistics
Matches: 164, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
88 47 0.29
89 63 0.38
90 28 0.17
91 6 0.04
92 20 0.12
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (88 bp):
AAAAATGAATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTGGGAAGTTTGAGGGTAAAAATG
GAATTTTTGGAAGTTTTAAGGTC
Found at i:6173 original size:13 final size:13
Alignment explanation
Indices: 6157--6195 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
6147 TTCTTTTTAT
*
6157 TAATAATTAATAC
1 TAATTATTAATAC
*
6170 TAATTATTAATAA
1 TAATTATTAATAC
*
6183 TTATTATTAATAC
1 TAATTATTAATAC
6196 AGTTATCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATTATTAATAC
Found at i:6186 original size:10 final size:10
Alignment explanation
Indices: 6153--6193 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
6143 CTTTTTCTTT
6153 TTATTAATAA
1 TTATTAATAA
* *
6163 TTAATACTAA
1 TTATTAATAA
6173 TTATTAATAA
1 TTATTAATAA
*
6183 TTATTATTAA
1 TTATTAATAA
6193 T
1 T
6194 ACAGTTATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
TTATTAATAA
Found at i:6878 original size:14 final size:14
Alignment explanation
Indices: 6859--6889 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
6849 GAGTTTTGTA
6859 ATTTTGTATTGGAC
1 ATTTTGTATTGGAC
6873 ATTTTGTATTGGAC
1 ATTTTGTATTGGAC
6887 ATT
1 ATT
6890 ATTTAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (14 bp):
ATTTTGTATTGGAC
Found at i:6910 original size:17 final size:16
Alignment explanation
Indices: 6890--6960 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 16
6880 ATTGGACATT
*
6890 ATTTAAATGAATTTTAA
1 ATTTAAAT-AAATTTAA
** *
6907 ATTTAAATTTATAATAA
1 ATTTAAATAAAT-TTAA
6924 ATTTAAATAAATTTAA
1 ATTTAAATAAATTTAA
6940 ATTTAAAATAAATTTAA
1 ATTT-AAATAAATTTAA
6957 ATTT
1 ATTT
6961 GTTGTGCCAG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
16 8 0.18
17 37 0.82
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (16 bp):
ATTTAAATAAATTTAA
Found at i:6913 original size:6 final size:6
Alignment explanation
Indices: 6902--6960 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
6892 TTAAATGAAT
6902 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
6947 -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
6961 GTTGTGCCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
4 6 0.13
5 6 0.13
6 31 0.69
7 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:6924 original size:11 final size:10
Alignment explanation
Indices: 6890--6958 Score: 63
Period size: 10 Copynumber: 6.8 Consensus size: 10
6880 ATTGGACATT
6890 ATTTAAATGAA
1 ATTTAAAT-AA
*
6901 TTTTAAATTTAA
1 ATTTAAA--TAA
6913 ATTTATAATAA
1 ATTTA-AATAA
6924 ATTTAAATAA
1 ATTTAAATAA
6934 ATTTAAAT--
1 ATTTAAATAA
*
6942 -TTAAAATAA
1 ATTTAAATAA
6951 ATTTAAAT
1 ATTTAAAT
6959 TTGTTGTGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
7 6 0.12
10 19 0.40
11 14 0.29
12 6 0.12
13 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:6934 original size:27 final size:27
Alignment explanation
Indices: 6904--6958 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
6894 AAATGAATTT
*
6904 TAAATTTAAATTTATAATAAATTTAAA
1 TAAATTTAAATTTAAAATAAATTTAAA
6931 TAAATTTAAATTTAAAATAAATTTAAA
1 TAAATTTAAATTTAAAATAAATTTAAA
6958 T
1 T
6959 TTGTTGTGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATTTAAATTTAAAATAAATTTAAA
Found at i:25244 original size:2 final size:2
Alignment explanation
Indices: 25231--25266 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
25221 TGAATTGTGG
25231 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25267 TGTTGAAGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25359 original size:6 final size:6
Alignment explanation
Indices: 25339--25401 Score: 67
Period size: 6 Copynumber: 10.7 Consensus size: 6
25329 TTAAATTGGC
** *
25339 TTAAAT TTATTT TTAAAT TTAAAT TT--AT CTTAAAT TTAAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT
*
25386 GTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAA
25402 TCAAATTTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
6 40 0.87
7 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:25371 original size:29 final size:29
Alignment explanation
Indices: 25338--25394 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
25328 TTTAAATTGG
** **
25338 CTTAAATTTATTTTTAAATTTAAATTTAT
1 CTTAAATTTAAATTTAAAAGTAAATTTAT
25367 CTTAAATTTAAATTTAAAAGTAAATTTA
1 CTTAAATTTAAATTTAAAAGTAAATTTA
25395 AATTTAATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (29 bp):
CTTAAATTTAAATTTAAAAGTAAATTTAT
Found at i:25373 original size:17 final size:18
Alignment explanation
Indices: 25339--25382 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
25329 TTAAATTGGC
*
25339 TTAAATTTATTTTTAAAT
1 TTAAATTTATTCTTAAAT
25357 TTAAATTTA-TCTTAAAT
1 TTAAATTTATTCTTAAAT
25374 TTAAATTTA
1 TTAAATTTA
25383 AAAGTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTTATTCTTAAAT
Found at i:26194 original size:3 final size:3
Alignment explanation
Indices: 26188--26236 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
26178 AATGTGCTAT
* * *
26188 TAA TAA TAT TAA TAA TAA TAA TAT TAA TAA TAA TTAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
26234 TAA
1 TAA
26237 ATAAAAAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:27001 original size:17 final size:18
Alignment explanation
Indices: 26976--27009 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
26966 CTTTTTCTGA
*
26976 TTTTTATAC-TTTAATTC
1 TTTTCATACTTTTAATTC
26993 TTTTCATACTTTTAATT
1 TTTTCATACTTTTAATT
27010 AATTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTCATACTTTTAATTC
Done.