Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009200.1 Kokia drynarioides strain JFW-HI SEQ_123905, 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: 24739
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Found at i:6615 original size:39 final size:39
Alignment explanation
Indices: 6554--6640 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 39
6544 TCAAAATCTA
* *
6554 AAATATTTTGAAAATGGAGGAAGATTGTTGGAACTTTTTC
1 AAATA-TTTGAAAATGGAGGAAGATTATTGGAACATTTTC
6594 AAATATTTGAAAAT-GAGGGAAGATTATTGGAACATTTTC
1 AAATATTTGAAAATGGA-GGAAGATTATTGGAACATTTTC
6633 AAATATTT
1 AAATATTT
6641 ATAGTGTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 2 0.05
39 37 0.84
40 5 0.11
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.37
Consensus pattern (39 bp):
AAATATTTGAAAATGGAGGAAGATTATTGGAACATTTTC
Found at i:7839 original size:261 final size:257
Alignment explanation
Indices: 7219--7902 Score: 749
Period size: 261 Copynumber: 2.7 Consensus size: 257
7209 TTTTACTAAC
* * * * * *
7219 ATAATAATTGGTTGAACTATCTTATGTTATTTTATCGCCTATCAATTTATCAAATCTCTATAAGG
1 ATAATAATTGATTGAACTATCTTATGTTATCTTATCGCATGTCAGTTTATCAAATCCCTATAAGG
* * * *
7284 -TCAATGAGAA-TTG-GG-G---AG--T-ACTTCAT-AGTTTTACTCTTGATAAATAATGTTGCA
66 AT-AATGA-AACTTGAGGAGTTTTGTTTCACTACTTCAGTTATACTCTTGATAAATAATGTTGCA
*** *
7338 TCTTGCAAAATTGGAAAAAACCAATTTTTTAATATGATACTTTTAGAGAATATATATAAGGTAAC
129 TCCAACAAAATTGAAAAAAACCAATTTTTTAATATGATACTTTTAGAGAATATATATAAGGTAAC
* * *** *
7403 GACAAGGTGAGGTGGCACCATGTTTTGGAAGTTGCTTTCGATGTGCGGGAAAAATGTGCGGTAT
194 GACAAGGTGAGGTGGCACCATGTTGTGGAAGTTGCTTTAGATGTGCGGGAAAAATACACAGTAT
* * * *
7467 ATAATAATTGGTTGAACTATCTTATGTTATTTTATCGCATGTTAGTTTATCAAATCTCTATAAGG
1 ATAATAATTGATTGAACTATCTTATGTTATCTTATCGCATGTCAGTTTATCAAATCCCTATAAGG
*
7532 TTAATGAAACTTGAGGAGTTTTGTTTCACTACTTCACGATTATACTCTTGATAAATAATGTTGCA
66 ATAATGAAACTTGAGGAGTTTTGTTTCACTACTTCA-G-TTATACTCTTGATAAATAATGTTGCA
7597 TCCAACAAAATT-AAAAAAACAAACAATTTTTTAATATGATACGCTTTTAGAGAATATATATAAG
129 TCCAACAAAATTGAAAAAAAC---CAATTTTTTAATATGATA--CTTTTAGAGAATATATATAAG
*
7661 GTAACGACAAGGTGAGGTGGCACCATGTTGTGGAAGTTGCTTTAGATGTGC-GGAAAAATACATA
189 GTAACGACAAGGTGAGGTGGCACCATGTTGTGGAAGTTGCTTTAGATGTGCGGGAAAAATACACA
*
7725 GTGT
254 GTAT
* *
7729 ATAATAATTGATTGAACTATTTTATGTTATCTTATC-CTTGTCAGTTTATCAAATCCCTATAAGG
1 ATAATAATTGATTGAACTATCTTATGTTATCTTATCGCATGTCAGTTTATCAAATCCCTATAAGG
** * *
7793 ATAATGTGACTT-ACGGAGTTTTGTTTCACTATTTTGCAGTTATACTCTTAATAAA-AATGCTT-
66 ATAATGAAACTTGA-GGAGTTTTGTTTCACTA-CTT-CAGTTATACTCTTGATAAATAATG-TTG
* * * * * *
7855 CACCCTACAAACTTG-ACAAAATC-ATTTTTTAATAAGATATACTTTTAG
127 CATCCAACAAAATTGAAAAAAACCAATTTTTTAATATG--ATACTTTTAG
7903 GTGTTGTTTG
Statistics
Matches: 374, Mismatches: 37, Indels: 42
0.83 0.08 0.09
Matches are distributed among these distances:
247 2 0.01
248 69 0.18
249 3 0.01
250 1 0.00
253 1 0.00
255 1 0.00
256 24 0.06
257 2 0.01
258 11 0.03
259 34 0.09
260 21 0.06
261 86 0.23
262 47 0.13
263 72 0.19
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (257 bp):
ATAATAATTGATTGAACTATCTTATGTTATCTTATCGCATGTCAGTTTATCAAATCCCTATAAGG
ATAATGAAACTTGAGGAGTTTTGTTTCACTACTTCAGTTATACTCTTGATAAATAATGTTGCATC
CAACAAAATTGAAAAAAACCAATTTTTTAATATGATACTTTTAGAGAATATATATAAGGTAACGA
CAAGGTGAGGTGGCACCATGTTGTGGAAGTTGCTTTAGATGTGCGGGAAAAATACACAGTAT
Found at i:9255 original size:63 final size:62
Alignment explanation
Indices: 9153--9271 Score: 184
Period size: 63 Copynumber: 1.9 Consensus size: 62
9143 CTCAAAGTTA
* *
9153 CAACCTTTGTCACTTCTAGTCCTTATAATAGTGCCAATGTTACTACATTTCTCATTCGTTGCT
1 CAACCTTTGTCACTTCTAATCCTTACAATAGTGCCAATGTTACTAC-TTTCTCATTCGTTGCT
* * *
9216 CAACCTTTGTGACTTCTAATCCTTACAATAGTGCTAATGTTACTACTTTCTTATTC
1 CAACCTTTGTCACTTCTAATCCTTACAATAGTGCCAATGTTACTACTTTCTCATTC
9272 ATTAGCTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 9 0.18
63 42 0.82
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (62 bp):
CAACCTTTGTCACTTCTAATCCTTACAATAGTGCCAATGTTACTACTTTCTCATTCGTTGCT
Found at i:10212 original size:58 final size:59
Alignment explanation
Indices: 10144--10526 Score: 219
Period size: 57 Copynumber: 6.6 Consensus size: 59
10134 ACCCGGGGGA
* * *
10144 AAAATGGTAATTTTGGGAAAGTTCGA-GATCAAAATGGAATTTTTAGAAGTTCGAGGGT
1 AAAATGGTAATTTTGGGAAAGTTCGAGGGTAAAAATGGAATTTTTAAAAGTTCGAGGGT
* * * ** *
10202 AAAATTGTAATTTTTGAAAAAATCGA-GGTCAAAAATGGAAATTTTAAAAGTTC-AGGGGT
1 AAAATGGTAATTTTGGGAAAGTTCGAGGGT-AAAAATGGAATTTTTAAAAGTTCGA-GGGT
* * * *
10261 AAAATGGTAATTTTTTGTGAAA--TC-AGGGTAAAAATGGGATTATAAAAAGTTCGAGGGT
1 AAAATGGTAA--TTTTGGGAAAGTTCGAGGGTAAAAATGGAATTTTTAAAAGTTCGAGGGT
* * *
10319 AAAAT-ATAATTTT-GGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAA-AT--AGGGT
1 AAAATGGTAATTTTGGGAAAGTTCGAGGGTAAAAATGGAATTTTT--AAAAGTTCGAGGGT
* * * * ** ** *
10375 CAAAATGG-GATTTT-TGAAAGTTTGGGGGTAAAAATATAATTTTGGAAAGTTTG-GGGT
1 -AAAATGGTAATTTTGGGAAAGTTCGAGGGTAAAAATGGAATTTTTAAAAGTTCGAGGGT
* * * * * *
10432 AATAT-GTAATTTTTAGG-AAGTT-GAAGGGTAAAAATGTAATTTTTAAGAAATTCAAGGAT
1 AAAATGGTAA-TTTTGGGAAAGTTCG-AGGGTAAAAATGGAATTTTTAA-AAGTTCGAGGGT
* * *
10491 AAAAAT-GTAATTTTTAGG-AAGTTCGAGAGCAAAAAT
1 -AAAATGGTAA-TTTTGGGAAAGTTCGAGGGTAAAAAT
10527 ATAATTTTCA
Statistics
Matches: 254, Mismatches: 47, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
54 4 0.02
55 8 0.03
56 14 0.06
57 85 0.33
58 59 0.23
59 46 0.18
60 30 0.12
61 8 0.03
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTGGGAAAGTTCGAGGGTAAAAATGGAATTTTTAAAAGTTCGAGGGT
Found at i:10284 original size:59 final size:58
Alignment explanation
Indices: 10144--10331 Score: 174
Period size: 59 Copynumber: 3.2 Consensus size: 58
10134 ACCCGGGGGA
* * * *
10144 AAAATGGTAA-TTTTGGGAAAGTTCGAGATC-AAAATGGAATTTTTAGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGAGAAA--TCGAGGTCAAAAATGGAAATTTTAAAAGTTCGAGGGT
* *
10202 AAAATTGTAATTTTTGAAAAAATCGAGGTCAAAAATGGAAATTTTAAAAGTTC-AGGGGT
1 AAAATGGTAATTTTTG-AGAAATCGAGGTCAAAAATGGAAATTTTAAAAGTTCGA-GGGT
* * *
10261 AAAATGGTAATTTTTTGTGAAATC-AGGGT-AAAAATGG-GATTATAAAAAGTTCGAGGGT
1 AAAATGGTAA-TTTTTGAGAAATCGA-GGTCAAAAATGGAAATT-TTAAAAGTTCGAGGGT
*
10319 AAAAT-ATAATTTT
1 AAAATGGTAATTTT
10332 GGAAAGTTCG
Statistics
Matches: 110, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
56 4 0.04
57 6 0.05
58 44 0.40
59 47 0.43
60 9 0.08
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTTGAGAAATCGAGGTCAAAAATGGAAATTTTAAAAGTTCGAGGGT
Found at i:10364 original size:30 final size:30
Alignment explanation
Indices: 10143--10566 Score: 235
Period size: 30 Copynumber: 14.5 Consensus size: 30
10133 TACCCGGGGG
* *
10143 AAAAATGGTAATTTTGGGAAAGTTCGA-GAT
1 AAAAAT-GTAATTTTTGGAAAGTTCGAGGGT
* * *
10173 CAAAATGGAATTTTTAG-AAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAAGTTCGAGGGT
* * **
10202 AAAATTGTAATTTTTGAAAAAATCGA-GGT
1 AAAAATGTAATTTTTGGAAAGTTCGAGGGT
* * *
10231 CAAAAATGGAAATTTT-AAAAGTTC-AGGGGT
1 -AAAAATGTAATTTTTGGAAAGTTCGA-GGGT
10261 -AAAATGGTAATTTTTTGTGAAA--TC-AGGGT
1 AAAAAT-GTAA-TTTTTG-GAAAGTTCGAGGGT
** * **
10290 AAAAATGGGA-TTATAAAAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAAGTTCGAGGGT
*
10319 -AAAATATAA-TTTTGGAAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAAGTTCGAGGGT
**
10347 AAAAATGTAATTTTTGGAAAAAT--AGGGT
1 AAAAATGTAATTTTTGGAAAGTTCGAGGGT
* ** * *
10375 CAAAATGGGATTTTT-GAAAGTTTGGGGGT
1 AAAAATGTAATTTTTGGAAAGTTCGAGGGT
* *
10404 AAAAATATAA-TTTTGGAAAGTTTG-GGGT
1 AAAAATGTAATTTTTGGAAAGTTCGAGGGT
*
10432 -AATATGTAATTTTTAGG-AAGTT-GAAGGGT
1 AAAAATGTAATTTTT-GGAAAGTTCG-AGGGT
* * *
10461 AAAAATGTAATTTTTAAGAAA-TTCAAGGAT
1 AAAAATGTAATTTTT-GGAAAGTTCGAGGGT
* *
10491 AAAAATGTAATTTTTAGG-AAGTTCGAGAGC
1 AAAAATGTAATTTTT-GGAAAGTTCGAGGGT
* *** * *
10521 AAAAATATAATTTTCAAAAAGTTTGAGGAT
1 AAAAATGTAATTTTTGGAAAGTTCGAGGGT
* *
10551 CAAAATATAATTTTTG
1 AAAAATGTAATTTTTG
10567 CACAGTTTAG
Statistics
Matches: 301, Mismatches: 66, Indels: 54
0.71 0.16 0.13
Matches are distributed among these distances:
26 3 0.01
27 16 0.05
28 72 0.24
29 80 0.27
30 125 0.42
31 2 0.01
32 3 0.01
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.33
Consensus pattern (30 bp):
AAAAATGTAATTTTTGGAAAGTTCGAGGGT
Found at i:12266 original size:6 final size:6
Alignment explanation
Indices: 12251--12341 Score: 80
Period size: 6 Copynumber: 15.7 Consensus size: 6
12241 TGTAATTGAT
* * * *
12251 TTTAAA TTTAAG TTTAAA ATT-AT TTTAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * *
12297 TTTAAA TTCATT TTTAAA TTTAAA TTTAAA -GTAAA TTTAAT TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
12342 GAAATAAATC
Statistics
Matches: 65, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
5 11 0.17
6 54 0.83
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:12292 original size:34 final size:35
Alignment explanation
Indices: 12253--12320 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 35
12243 TAATTGATTT
*
12253 TAAATTTAAGTTTAAAATT-A-TTTTAAATTTAAAC
1 TAAATTTAAATTT-AAATTCATTTTTAAATTTAAAC
12287 TAAATTTAAATTTAAATTCATTTTTAAATTTAAA
1 TAAATTTAAATTTAAATTCATTTTTAAATTTAAA
12321 TTTAAAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 5 0.16
34 13 0.42
35 13 0.42
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
TAAATTTAAATTTAAATTCATTTTTAAATTTAAAC
Found at i:12312 original size:18 final size:17
Alignment explanation
Indices: 12252--12322 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
12242 GTAATTGATT
* *
12252 TTAAATTTAAGTTTAAAA
1 TTAATTTTAAATTT-AAA
12270 TT-ATTTTAAATTTAAA
1 TTAATTTTAAATTTAAA
* *
12286 CTAAATTTAAATTTAAA
1 TTAATTTTAAATTTAAA
*
12303 TTCATTTTTAAATTTAAA
1 TT-AATTTTAAATTTAAA
12321 TT
1 TT
12323 TAAAGTAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
16 4 0.09
17 23 0.52
18 17 0.39
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
TTAATTTTAAATTTAAA
Found at i:12333 original size:17 final size:18
Alignment explanation
Indices: 12311--12355 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
12301 AATTCATTTT
*
12311 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
12328 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
*
12346 TAAATCTAAA
1 TAAATTTAAA
12356 ACCCATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:13453 original size:16 final size:16
Alignment explanation
Indices: 13434--13471 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
13424 TATTAATTAA
*
13434 ATATTAACATCACATT
1 ATATTAACATCAAATT
*
13450 ATATTATCATCAAATT
1 ATATTAACATCAAATT
13466 A-ATTAA
1 ATATTAA
13472 TTTGGTTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATTAACATCAAATT
Found at i:13748 original size:43 final size:43
Alignment explanation
Indices: 13696--13818 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
13686 CTTTAGCGGA
13696 GGCGTTTGTGGGGAAAGCGTCGCTAAAGATCATGTTCTTTAAC
1 GGCGTTTGTGGGGAAAGCGTCGCTAAAGATCATGTTCTTTAAC
* * * * *
13739 GGCGTTTGTGGGGAAAGAGCCGCTAAAAACCATGTTCTTTAGC
1 GGCGTTTGTGGGGAAAGCGTCGCTAAAGATCATGTTCTTTAAC
*
13782 GGCGTTTGT--GGATAAGCGTCGTTAAAGATCATGTTCT
1 GGCGTTTGTGGGGA-AAGCGTCGCTAAAGATCATGTTCT
13819 ATAGCGACCT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 3 0.04
42 19 0.28
43 47 0.68
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (43 bp):
GGCGTTTGTGGGGAAAGCGTCGCTAAAGATCATGTTCTTTAAC
Found at i:14370 original size:23 final size:21
Alignment explanation
Indices: 14327--14371 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
14317 TATTGTGAAT
* *
14327 TTAAAAATTAAAAACAGATAA
1 TTAAAAATAAAAAACACATAA
14348 TTAAAAATAAATAGAACACATAA
1 TTAAAAATAAA-A-AACACATAA
14371 T
1 T
14372 AATCTCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 1 0.05
23 9 0.45
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.24
Consensus pattern (21 bp):
TTAAAAATAAAAAACACATAA
Found at i:21852 original size:22 final size:22
Alignment explanation
Indices: 21823--21865 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
21813 TCTCTTTACC
21823 GTTATGGGA-TGCTTTATTTCT
1 GTTATGGGATTGCTTTATTTCT
*
21844 GTTACTGGGATTGTTTTATTTC
1 GTTA-TGGGATTGCTTTATTTC
21866 AGTGTCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 10 0.53
ACGTcount: A:0.14, C:0.09, G:0.23, T:0.53
Consensus pattern (22 bp):
GTTATGGGATTGCTTTATTTCT
Found at i:22203 original size:24 final size:24
Alignment explanation
Indices: 22171--22222 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
22161 TTTCTAAAAG
*
22171 ATTTGGTATTTATTAGTATAATAT
1 ATTTGGTATTTATTAGCATAATAT
* *
22195 ATTTTGTATTTATTAGCATAATTT
1 ATTTGGTATTTATTAGCATAATAT
22219 ATTT
1 ATTT
22223 AACTTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (24 bp):
ATTTGGTATTTATTAGCATAATAT
Found at i:24136 original size:24 final size:24
Alignment explanation
Indices: 24109--24154 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24099 AAGATTTAGT
**
24109 ATTTATTAGTATAATATATTTTGC
1 ATTTATTAACATAATATATTTTGC
*
24133 ATTTATTAACATAATTTATTTT
1 ATTTATTAACATAATATATTTT
24155 ACTTAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTTATTAACATAATATATTTTGC
Done.