Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010241.1 Kokia drynarioides strain JFW-HI SEQ_125073, 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: 59155
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 175 characters in sequence are not A, C, G, or T
Found at i:594 original size:29 final size:28
Alignment explanation
Indices: 555--883 Score: 182
Period size: 29 Copynumber: 11.3 Consensus size: 28
545 NNNACCCTGA
*
555 AACTTCTAAAAATTACATTTTACCCCTCG
1 AACTTCCAAAAATTACATTTTA-CCCTCG
* *
584 AACTTTCAAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTACA-TTTT-ACCCTCG
* *
613 AAACTTCCAAAAAATACATTTTACCCTTG
1 -AACTTCCAAAAATTACATTTTACCCTCG
* **
642 AACTTCCAAAAATTCCATTTTTAACCC-AA
1 AACTTCCAAAAATTACA-TTTT-ACCCTCG
** * *
671 AACTTTTAAAAATTACTTTTTTATCCTCG
1 AACTTCCAAAAATTAC-ATTTTACCCTCG
* ** *
700 AACTTCCAAACATTTTATTTTTAACCTCG
1 AACTTCCAAAAATTACA-TTTTACCCTCG
*** *
729 AAACTTTTGAAAATTACATTTTTACCCTTG
1 -AACTTCCAAAAATTACA-TTTTACCCTCG
* * *
759 AACTTCCAAAAATTCCATTTTTGA-CTTTG
1 AACTTCCAAAAATTACA-TTTT-ACCCTCG
*
788 AAACTTTCAAAAATTACATTTTTACCCTCG
1 -AACTTCCAAAAATTACA-TTTTACCCTCG
* **
818 AA-TGTCCAAAAACT-CTATTTTGACCCTAA
1 AACT-TCCAAAAATTAC-ATTTT-ACCCTCG
** *
847 AACTTTTAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATTA-CATTTTACCCTCG
*
876 AACATCCA
1 AACTTCCA
884 CAAGTTTCAT
Statistics
Matches: 226, Mismatches: 55, Indels: 38
0.71 0.17 0.12
Matches are distributed among these distances:
28 25 0.11
29 126 0.56
30 73 0.32
31 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (28 bp):
AACTTCCAAAAATTACATTTTACCCTCG
Found at i:751 original size:59 final size:59
Alignment explanation
Indices: 553--897 Score: 360
Period size: 59 Copynumber: 5.9 Consensus size: 59
543 NNNNNACCCT
* * *
553 GAAACTTCTAAAAATTACA-TTTTACCCCTCGAACTTTCAAAAATTCCATTTTTGACCTC
1 GAAACTTTTAAAAATTACATTTTTA-CCCTCGAACTTCCAAAAATTCCATTTTTAACCTC
** * *
612 GAAACTTCCAAAAAATACA-TTTTACCCTTGAACTTCCAAAAATTCCATTTTTAACC-C
1 GAAACTTTTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTC
* * * * **
669 AAAACTTTTAAAAATTACTTTTTTATCCTCGAACTTCCAAACATTTTATTTTTAACCTC
1 GAAACTTTTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTC
* * * * *
728 GAAACTTTTGAAAATTACATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACTTT
1 GAAACTTTTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTC
* * * * *
787 GAAACTTTCAAAAATTACATTTTTACCCTCGAA-TGTCCAAAAACTCTATTTTGACCCT-
1 GAAACTTTTAAAAATTACATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTAACCTC
* * * * * *
845 AAAACTTTTAAAAATTACCA-TTTTACCCCCGAACATCCACAAGTTTCATTTTT
1 GAAACTTTTAAAAATTA-CATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT
898 TATCCTGATT
Statistics
Matches: 236, Mismatches: 45, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
57 15 0.06
58 101 0.43
59 120 0.51
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (59 bp):
GAAACTTTTAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTC
Found at i:2173 original size:52 final size:53
Alignment explanation
Indices: 2085--2277 Score: 207
Period size: 52 Copynumber: 3.7 Consensus size: 53
2075 ATTTCACTTC
* * * *
2085 ATTCATATACTCATGATGACACATAGCCATCAGACCTTATAATCCACT-AGGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTTATAATCCACTAAAGG
* * * * *
2137 ATTCGTACT-CTCACGATGATACAGAGTCATCGGACCTCATAATCC-GTAAAGG
1 ATTCATA-TACTCACGATGACACATAGTCATCGGACCTTATAATCCACTAAAGG
*
2189 ATTCATATACTCACGATGACACTTAGTCATCGGACCTT-TAAATCCA-TAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTTAT-AATCCACTAAAGG
* * *
2241 ATTTCATATACTTACGATAACACTTAGTCATCGGACC
1 A-TTCATATACTCACGATGACACATAGTCATCGGACC
2278 CTTTTTCATT
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
51 3 0.03
52 82 0.69
53 34 0.29
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (53 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTTATAATCCACTAAAGG
Found at i:6371 original size:150 final size:146
Alignment explanation
Indices: 6055--6706 Score: 772
Period size: 148 Copynumber: 4.5 Consensus size: 146
6045 GATTTTGGGA
* * * *
6055 AAAGTTTT-ATTTTTTTAAACAATTTCGAAATAAAAACTTT-GATTTTTAAGTAAAATAGTGATT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAAT-AAAAGTTTAGATTTTTAAATAAAATAGTGATT
* * * * *
6118 TTCTTTAAAACAGAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTCTAG---------AAA
65 TTCATTAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAAA
*** *
6174 CGTTTAAATTTTTTAAAC
130 AAATTAAA-TTTTTAAAT
*
6192 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAATAAAATAGTGATTT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAATAAAATAGTGATTT
* * *
6257 TCTTTAAAAAAAAAAGAATAAGTTTATATTTTTAAAATTAAAAATTTGTTTTTTAGTTA-TTTAA
66 TCATT--AAAAAAAAG-A-AAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAA
6321 AAAAAATTAAATTTTTAAAT
127 AAAAAATTAAATTTTTAAAT
* *
6341 AAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAGTTTAGAATTTTAAATAAAGTAGTGATT
1 AAAGTTTTGA-TTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAATAAAATAGTGATT
* * *
6406 TTCATTAAAAAAAGAGAAAGTTTATATTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAA
65 TTCATTAAAAAAA-AGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTT-AAA
*
6471 AAAAATTAAAATTTTAAAT
128 AAAAATTAAATTTTTAAAT
* * * * * *
6490 AAAATTTTGATTTTTTTTAACTATTTCAAAATAAAAGTTTAAATTTTTAAGTAAAGTAATGATTT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAATAAAATAGTGATTT
* *
6555 TCATTAAAAAAAAGAAAGTTTAAATTTTTAAAAAATAAAAATATGTTTTTTAGTGATTTTAAAGA
66 TCATTAAAAAAAAGAAAGTTTATATTTTT-AAAAATAAAAATATGTTTTTTAGTTATTTTAAA-A
6620 AAAAGTTTAAATTTTTAAAT
129 AAAA--TTAAATTTTTAAAT
* * *
6640 AAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAATTTTGA-TTTTAAAGTAAAATAATGAT
1 AAAGTTTTGA-TTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAA-TAAAATAGTGAT
6704 TTT
64 TTT
6707 ATTTTAATCA
Statistics
Matches: 449, Mismatches: 42, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
137 15 0.03
138 49 0.11
140 7 0.02
141 1 0.00
142 33 0.07
147 54 0.12
148 105 0.23
149 50 0.11
150 92 0.20
151 43 0.10
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (146 bp):
AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAATAAAATAGTGATTT
TCATTAAAAAAAAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAAAA
AATTAAATTTTTAAAT
Found at i:7662 original size:20 final size:20
Alignment explanation
Indices: 7624--7662 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7614 TAGAATTTTG
* *
7624 AAGAATTTAAAATTTAGATC
1 AAGAATTTAAAAGTAAGATC
*
7644 AAGAATTTTAAAGTAAGAT
1 AAGAATTTAAAAGTAAGAT
7663 AAATCATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (20 bp):
AAGAATTTAAAAGTAAGATC
Found at i:8168 original size:231 final size:234
Alignment explanation
Indices: 7732--8205 Score: 666
Period size: 231 Copynumber: 2.0 Consensus size: 234
7722 TTAAATCTTT
* *
7732 TAAAATCAAAATAATAATAAAATATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTC
1 TAAAATCAAAATAATAATAAAAGATCGAATAAGTTGTAGATGAATTTCAATATTTCTCTTAATTC
* *
7797 ATTAGTAACTTTTAGGTTTTTTTTAGGATTCTAAAATAAAATAAATTTTAAGAATTGAAGGTATT
66 ATTAGTAA---TT--GTTTTTTTTAGAATTCTAAAATAAAATAAATTTTAAGAATTGAAAGTATT
* * *
7862 TTATTAGAATTATTGAAGTATCTTTTAGGGTTCTCGTTAGAAGTAAAAATCTCTAATTTAAGTTT
126 TTACTAGAATTATTGAAGTATCTTTCAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTT
* * *
7927 TAAGTTAGATAAATTTGGTGAACGCCTCTTAGTCAAGTTACAAG
191 TAAATTAGATAAATTTGATGAACACCTCTTAGTCAAGTTACAAG
* *
7971 TAAAA-CAAAGTAATGATAAAAGATCGAATAAGTTGTAGATGAATTTCAATATTTCTCTTAATTC
1 TAAAATCAAAATAATAATAAAAGATCGAATAAGTTGTAGATGAATTTCAATATTTCTCTTAATTC
* * *
8035 ATTAGTAA-T-TTTTTTTTAGAATTTTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACT
66 ATTAGTAATTGTTTTTTTTAGAATTCTAAAATAAAATAAATTTTAAGAATTGAAAGTATTTTACT
* * * * * *
8098 ATAATTATTTAGGTATCTTTCAGGGTTTTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAAT
131 AGAATTATTGAAGTATCTTTCAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAAT
* * *
8163 TAGATAAGTTTGATGAACACGTCTTAGTTAAGTTACAAG
196 TAGATAAATTTGATGAACACCTCTTAGTCAAGTTACAAG
8202 TAAA
1 TAAA
8206 TTAGAGGCAT
Statistics
Matches: 211, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
231 142 0.67
234 1 0.00
238 63 0.30
239 5 0.02
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (234 bp):
TAAAATCAAAATAATAATAAAAGATCGAATAAGTTGTAGATGAATTTCAATATTTCTCTTAATTC
ATTAGTAATTGTTTTTTTTAGAATTCTAAAATAAAATAAATTTTAAGAATTGAAAGTATTTTACT
AGAATTATTGAAGTATCTTTCAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAAT
TAGATAAATTTGATGAACACCTCTTAGTCAAGTTACAAG
Found at i:9296 original size:23 final size:23
Alignment explanation
Indices: 9270--9319 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
9260 AATTTTATAA
9270 CTAATTTGGGACTCTTCATGACG
1 CTAATTTGGGACTCTTCATGACG
* *
9293 CTAATTTGGGATTCTTCGTGACG
1 CTAATTTGGGACTCTTCATGACG
9316 CTAA
1 CTAA
9320 CTCAGTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (23 bp):
CTAATTTGGGACTCTTCATGACG
Found at i:11364 original size:25 final size:24
Alignment explanation
Indices: 11335--11383 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
11325 TTAATTTATT
11335 TAAATTTGTAATAATTTTTA-AAATA
1 TAAATTT-TAA-AATTTTTATAAATA
*
11360 TAAATTTTGAAATTTTTATAAATA
1 TAAATTTTAAAATTTTTATAAATA
11384 CTTTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 8 0.36
24 7 0.32
25 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TAAATTTTAAAATTTTTATAAATA
Found at i:14918 original size:26 final size:25
Alignment explanation
Indices: 14869--14919 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
14859 GTATATATGT
**
14869 TGTTTTTTTGTTAATTAGTTAAATA
1 TGTTTTTTTGTTAATTAGGAAAATA
*
14894 TGTTTTTTTTTTAATTTAGGAAAATA
1 TGTTTTTTTGTTAA-TTAGGAAAATA
14920 GATTGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (25 bp):
TGTTTTTTTGTTAATTAGGAAAATA
Found at i:20768 original size:19 final size:19
Alignment explanation
Indices: 20740--20786 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
20730 ATCGAATATT
20740 TTATATTATTTAT-TTTTA
1 TTATATTATTTATCTTTTA
20758 TTATCATTATTTATCTTTTA
1 TTAT-ATTATTTATCTTTTA
20778 -TA-ATTATTT
1 TTATATTATTT
20787 TTTAATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.26
18 4 0.15
19 11 0.41
20 5 0.19
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATTATTTATCTTTTA
Found at i:21411 original size:26 final size:26
Alignment explanation
Indices: 21355--21415 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
21345 AACCATTTAC
* *
21355 AGTTTACCATTTATTTTTCTACATTT
1 AGTTTATCATTTATTTTTCTACACTT
*
21381 AGTTTATCATTTATTTTT-TCGCACTT
1 AGTTTATCATTTATTTTTCT-ACACTT
*
21407 GGTTTATCA
1 AGTTTATCA
21416 ACTATTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 1 0.03
26 29 0.97
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (26 bp):
AGTTTATCATTTATTTTTCTACACTT
Found at i:26419 original size:3 final size:3
Alignment explanation
Indices: 26411--26440 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
26401 CAAAATCAAT
26411 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
26441 ATAGGTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31122 original size:29 final size:30
Alignment explanation
Indices: 31076--31155 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
31066 GAATCTGATC
*
31076 AAATCAAAATTTCATGTATAGAATTACACA-
1 AAATCAAAATTT-ATGTATACAATTACACAT
* *
31106 AAATTAAAATTTATGTATACAATTACATATT
1 AAATCAAAATTTATGTATACAATTACACA-T
*
31137 AAACCAAAATTTATGTATA
1 AAATCAAAATTTATGTATA
31156 ATTTCGAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.35
30 11 0.26
31 17 0.40
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTTATGTATACAATTACACAT
Found at i:40150 original size:46 final size:46
Alignment explanation
Indices: 40097--40187 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
40087 GGAAGCCAAA
40097 TGGAAGTTTTCTCTTGTACCTTCAAAACACTACAAATTTCTCGAAT
1 TGGAAGTTTTCTCTTGTACCTTCAAAACACTACAAATTTCTCGAAT
40143 TGGAAGTTTTCTCTTGTACCTTCAAAACACTACAAATTTCTCGAA
1 TGGAAGTTTTCTCTTGTACCTTCAAAACACTACAAATTTCTCGAA
40188 ATGTACACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (46 bp):
TGGAAGTTTTCTCTTGTACCTTCAAAACACTACAAATTTCTCGAAT
Found at i:41115 original size:12 final size:11
Alignment explanation
Indices: 41097--41136 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
41087 AAATAAATTT
41097 AATATTTTTTA
1 AATATTTTTTA
41108 ATATATTTTTTA
1 A-ATATTTTTTA
*
41120 GAATATTTATTA
1 -AATATTTTTTA
41132 AATAT
1 AATAT
41137 AGGGAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 6 0.23
12 19 0.73
13 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
AATATTTTTTA
Found at i:42148 original size:6 final size:6
Alignment explanation
Indices: 42137--42165 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42127 TTTTTACGGA
42137 AGGGTG AGGGTG AGGGTG AGGGTG AGGGT
1 AGGGTG AGGGTG AGGGTG AGGGTG AGGGT
42166 AATTGATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (6 bp):
AGGGTG
Done.