Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010689.1 Kokia drynarioides strain JFW-HI SEQ_125635, 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: 49756
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:124 original size:4 final size:4
Alignment explanation
Indices: 115--149 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
105 TTCTTCCTTG
*
115 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TT
150 ATTTTTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:131 original size:22 final size:22
Alignment explanation
Indices: 96--149 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
86 CTTCTTCGCC
*
96 TTCTTATCCTTCTTCCTTGT-TCT
1 TTCTT-TCTTTCTTCCTT-TCTCT
*
119 TTCTTTCTTTCTTTCTTTCTCT
1 TTCTTTCTTTCTTCCTTTCTCT
141 TT-TTTCTTT
1 TTCTTTCTTT
150 ATTTTTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.29
22 15 0.54
23 5 0.18
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70
Consensus pattern (22 bp):
TTCTTTCTTTCTTCCTTTCTCT
Found at i:13911 original size:3 final size:3
Alignment explanation
Indices: 13903--13932 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
13893 TGCTGACGAC
*
13903 CTG CTG CTG CTG CTG ATG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
13933 ATCTTCTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.30, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:13924 original size:15 final size:15
Alignment explanation
Indices: 13904--13934 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13894 GCTGACGACC
13904 TGCTGCTGCTGCTGA
1 TGCTGCTGCTGCTGA
13919 TGCTGCTGCTGCTGA
1 TGCTGCTGCTGCTGA
13934 T
1 T
13935 CTTCTGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.26, G:0.32, T:0.35
Consensus pattern (15 bp):
TGCTGCTGCTGCTGA
Found at i:13988 original size:11 final size:11
Alignment explanation
Indices: 13972--14009 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13962 AATTTCCTCT
13972 TTTCTTCTTCA
1 TTTCTTCTTCA
*
13983 TTTCTTCCTCA
1 TTTCTTCTTCA
*
13994 TTT-TTATTCA
1 TTTCTTCTTCA
14004 TTTCTT
1 TTTCTT
14010 GCCGACTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTCTTCTTCA
Found at i:14005 original size:21 final size:22
Alignment explanation
Indices: 13965--14009 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
13955 TCATTAAAAT
* *
13965 TTCCTCTTTTCTTCTTCATTTC
1 TTCCTCATTTCTTATTCATTTC
13987 TTCCTCATTT-TTATTCATTTC
1 TTCCTCATTTCTTATTCATTTC
14008 TT
1 TT
14010 GCCGACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (22 bp):
TTCCTCATTTCTTATTCATTTC
Found at i:18586 original size:37 final size:34
Alignment explanation
Indices: 18529--18611 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 34
18519 CCAACAAAAT
*
18529 AATAAAAATAAAGTTCAAAATAAAAATAAAATAA
1 AATAAAAATAAAGTTAAAAATAAAAATAAAATAA
* *
18563 AATAAAACATATAAGTCTAAAAATTAAAATAAAA-CA
1 AATAAAA-ATA-AAGT-TAAAAATAAAAATAAAATAA
18599 AATAACAAATAAA
1 AATAA-AAATAAA
18612 CAAAAGTACA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
34 7 0.17
35 5 0.12
36 13 0.31
37 17 0.40
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.20
Consensus pattern (34 bp):
AATAAAAATAAAGTTAAAAATAAAAATAAAATAA
Found at i:19776 original size:19 final size:20
Alignment explanation
Indices: 19749--19796 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
19739 AAATATAAAA
*
19749 TTTGAAATTTTTATAAA-TAT
1 TTTG-AATTTTTAAAAATTAT
19769 TTTGAA-TTTTAAAAATTAT
1 TTTGAATTTTTAAAAATTAT
19788 TTT-AATTTT
1 TTTGAATTTT
19797 CTTTTGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 10 0.40
19 11 0.44
20 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTGAATTTTTAAAAATTAT
Found at i:19778 original size:18 final size:18
Alignment explanation
Indices: 19757--19796 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
19747 AATTTGAAAT
*
19757 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTT-AA
19775 TTTTAAAAATTATTTTAA
1 TTTTAAAAATTATTTTAA
19793 TTTT
1 TTTT
19797 CTTTTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTAAAAATTATTTTAA
Found at i:20958 original size:9 final size:9
Alignment explanation
Indices: 20944--20969 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20934 TATAAAAATG
20944 CATTAAAAA
1 CATTAAAAA
20953 CATTAAAAA
1 CATTAAAAA
20962 CATTAAAA
1 CATTAAAA
20970 TAAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (9 bp):
CATTAAAAA
Found at i:22872 original size:25 final size:25
Alignment explanation
Indices: 22823--22902 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
22813 TTAGCTCTAT
* *
22823 CGAGCCTAGAAAGATTAACGCTCTTA
1 CGAGCC-AGAAAGAATATCGCTCTTA
*
22849 CGAGCCAGACAGAATATCGCTCTTA
1 CGAGCCAGAAAGAATATCGCTCTTA
*
22874 CAAGCCA-AATAGAATATCGCTCTTA
1 CGAGCCAGAA-AGAATATCGCTCTTA
22899 CGAG
1 CGAG
22903 ACAAAATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 1 0.02
25 40 0.85
26 6 0.13
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (25 bp):
CGAGCCAGAAAGAATATCGCTCTTA
Found at i:26433 original size:40 final size:40
Alignment explanation
Indices: 26389--26474 Score: 172
Period size: 40 Copynumber: 2.1 Consensus size: 40
26379 GTCGTATTTT
26389 TCGTATTATTGTATAAGACATGCATCTAATGATGTTTATC
1 TCGTATTATTGTATAAGACATGCATCTAATGATGTTTATC
26429 TCGTATTATTGTATAAGACATGCATCTAATGATGTTTATC
1 TCGTATTATTGTATAAGACATGCATCTAATGATGTTTATC
26469 TCGTAT
1 TCGTAT
26475 ACATTTACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (40 bp):
TCGTATTATTGTATAAGACATGCATCTAATGATGTTTATC
Found at i:29671 original size:15 final size:16
Alignment explanation
Indices: 29644--29673 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29634 GTCACTAACA
29644 TTTTAGATCATTTTTG
1 TTTTAGATCATTTTTG
29660 TTTTAG-TCATTTTT
1 TTTTAGATCATTTTT
29674 CGTTAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (16 bp):
TTTTAGATCATTTTTG
Found at i:33260 original size:57 final size:57
Alignment explanation
Indices: 33150--33261 Score: 138
Period size: 57 Copynumber: 2.0 Consensus size: 57
33140 ATAAGGTAAA
* * *
33150 AAAAAAATATCTTTTTGTTCATGTTTTTTAGTGTTGGTCATTAATTGTAAAACATTC
1 AAAAAAATATCTTTTTATTCATGTTTTTTAGTATTGGTCATTAACTGTAAAACATTC
* * *
33207 AAAAAAATAT-TTTTCTATTCGTGTTTTTTTA-TATTGGTCATTAGCTGTCAAACAT
1 AAAAAAATATCTTTT-TATTCATG-TTTTTTAGTATTGGTCATTAACTGTAAAACAT
33262 CTAAATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 4 0.09
57 36 0.77
58 7 0.15
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (57 bp):
AAAAAAATATCTTTTTATTCATGTTTTTTAGTATTGGTCATTAACTGTAAAACATTC
Found at i:38997 original size:13 final size:13
Alignment explanation
Indices: 38981--39008 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38971 AAACTCTATT
38981 TTTAGGATTAATA
1 TTTAGGATTAATA
38994 TTTAGGATTAATA
1 TTTAGGATTAATA
39007 TT
1 TT
39009 ATTATATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTAGGATTAATA
Found at i:40225 original size:13 final size:13
Alignment explanation
Indices: 40188--40246 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 13
40178 TTAGCAAATT
*
40188 TTTTTAT-TTTAT
1 TTTTTATATTTAA
*
40200 TATTTTATTATTTGCA
1 T-TTTTA-TATTT-AA
40216 TTTTTA-ATTTAA
1 TTTTTATATTTAA
40228 TTTTTATATTTTAA
1 TTTTTATA-TTTAA
40242 TTTTT
1 TTTTT
40247 TTCCTTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
12 8 0.21
13 10 0.26
14 11 0.29
15 8 0.21
16 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTATATTTAA
Found at i:43162 original size:30 final size:28
Alignment explanation
Indices: 43122--43198 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 28
43112 CAGTACATTT
*
43122 ATTTTTATTTTTATTTTTATT-TTCGTGTTC
1 ATTTTCATTTTTATTTTT-TTATT--TGTTC
*
43152 ATTTTCATTTTTCATTTTTTTCATTTTTTC
1 ATTTTCATTTTT-ATTTTTTT-ATTTGTTC
43182 ATTTTCATTTTTATTTT
1 ATTTTCATTTTTATTTT
43199 AAGTTTTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 5 0.12
30 29 0.69
31 6 0.14
32 2 0.05
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (28 bp):
ATTTTCATTTTTATTTTTTTATTTGTTC
Found at i:43174 original size:16 final size:17
Alignment explanation
Indices: 43153--43186 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
43143 TTCGTGTTCA
43153 TTTTCA-TTTTTCATTT
1 TTTTCATTTTTTCATTT
43169 TTTTCATTTTTTCATTT
1 TTTTCATTTTTTCATTT
43186 T
1 T
43187 CATTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCATTTTTTCATTT
Found at i:43178 original size:8 final size:8
Alignment explanation
Indices: 43153--43186 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
43143 TTCGTGTTCA
43153 TTTTCA-T
1 TTTTCATT
43160 TTTTCATTT
1 TTTTCA-TT
43169 TTTTCATT
1 TTTTCATT
43177 TTTTCATT
1 TTTTCATT
43185 TT
1 TT
43187 CATTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.24
8 12 0.48
9 7 0.28
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:43253 original size:12 final size:12
Alignment explanation
Indices: 43190--43254 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
43180 TCATTTTCAT
*
43190 TTTTATTTTAAG
1 TTTTAATTTAAG
*
43202 TTTTAATTTTAG
1 TTTTAATTTAAG
* *
43214 TTTTAGTTTTAG
1 TTTTAATTTAAG
* **
43226 TTTTAGTTTATTT
1 TTTTAATTTA-AG
43239 TTTTAATTTAA-
1 TTTTAATTTAAG
43250 TTTTA
1 TTTTA
43255 TTATGTAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
11 5 0.11
12 30 0.68
13 9 0.20
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTTAATTTAAG
Found at i:43273 original size:6 final size:6
Alignment explanation
Indices: 43119--43240 Score: 70
Period size: 6 Copynumber: 20.5 Consensus size: 6
43109 AATCAGTACA
** * * *
43119 TTTATT TTTATT TTTATT TTTATT TTCGTG TTCATT TTCATT TTTCATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT-ATT
* * * * * * *
43168 TTT-TT CATT-TT TTCATT TTCATT TTTATT TTAAGT TTTAAT TTTAGT
1 TTTATT -TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* * *
43215 TTTAGT TTTAGT TTTA-G TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
43241 TTAATTTAAT
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
5 7 0.07
6 82 0.86
7 6 0.06
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (6 bp):
TTTATT
Found at i:44239 original size:27 final size:26
Alignment explanation
Indices: 44205--44256 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
44195 AGAACATTTG
44205 ATTGAAAAAAAAGAAAAACAAAGAAA
1 ATTGAAAAAAAAGAAAAACAAAGAAA
* *
44231 ATTGAAAAAAGAAGAAGAAGAAAGAA
1 ATTGAAAAAA-AAGAAAAACAAAGAA
44257 GAACAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.08
Consensus pattern (26 bp):
ATTGAAAAAAAAGAAAAACAAAGAAA
Found at i:45335 original size:25 final size:23
Alignment explanation
Indices: 45294--45339 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
45284 CCAATTAAGA
45294 AATTATTATTTAGATTTAATTCT
1 AATTATTATTTAGATTTAATTCT
*
45317 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
45340 TGGATCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCT
Found at i:47697 original size:23 final size:23
Alignment explanation
Indices: 47666--47716 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
47656 GTCATAAGGT
* *
47666 AAAAA-CGTGTCATAAGACAGAG
1 AAAAAGCGTGCCACAAGACAGAG
* *
47688 GAAAAGCGTGCCACAAGATAGAG
1 AAAAAGCGTGCCACAAGACAGAG
47711 AAAAAG
1 AAAAAG
47717 TAAGTCACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.51, C:0.14, G:0.25, T:0.10
Consensus pattern (23 bp):
AAAAAGCGTGCCACAAGACAGAG
Found at i:48757 original size:21 final size:20
Alignment explanation
Indices: 48720--48761 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
48710 CCGGTGTCAT
48720 ATTCGTTTCCCCCAACAATG
1 ATTCGTTTCCCCCAACAATG
* *
48740 ATTCGATTTCTCCGAACAATG
1 ATTCG-TTTCCCCCAACAATG
48761 A
1 A
48762 ATGAGAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (20 bp):
ATTCGTTTCCCCCAACAATG
Done.