Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004526.1 Kokia drynarioides strain JFW-HI SEQ_117972, 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: 2448
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Found at i:131 original size:50 final size:49
Alignment explanation
Indices: 5--489 Score: 352
Period size: 50 Copynumber: 9.9 Consensus size: 49
1 AATT
* * * * *
5 CGGTACCATGAA-ATATGATGGGAATGGTTGAGGCCGTAACAGCGAACC
1 CGGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * *
53 CAGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAATGGCGAACC
1 CGGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * * * **
102 CGATACCTTAAAAGATTTGAAGGGAAAGGTTGATGCCGCAACGGTGAATT
1 CGGTACCAT-GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * * * **
152 AGGTACCTTAGAAGATGTGATA-GGAAAGATT-AGTCCACAACGGTGAATT
1 CGGTACCAT-GAAGATGTGA-AGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * ** *
201 CGGTACCATGAA-ATGTGATGGAAAAGGTTGAGGCAGCAATAGCGTACC
1 CGGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * ** *
249 CAGTACCATAAAGATTTGGAGGGAAAGGTTGAGGCCATAACGACGAACC
1 CGGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
** * * * *
298 TAGTACCTTAAAAGATGTGACGGGAAAGGTTGAGGCCGCAATGGCGAACC
1 CGGTACCAT-GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * ** *
348 CGGTACCTCAT-AAGATGTGATGGGAAAGATTGAGGCCGTAACAACGAATC
1 CGGTA-C-CATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * *
398 TGGTACCATGAA-ATGTGATGGGAAAGGTTGAGACCGTAATGGCGAACC
1 CGGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * *
446 CGGTGCCATGAAGATTTTAAGGGAAAGGTTGAGGCCGCAGCGGC
1 CGGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGC
490 AGGTACATTA
Statistics
Matches: 340, Mismatches: 86, Indels: 21
0.76 0.19 0.05
Matches are distributed among these distances:
47 13 0.04
48 76 0.22
49 117 0.34
50 130 0.38
51 2 0.01
52 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.20
Consensus pattern (49 bp):
CGGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
Found at i:338 original size:196 final size:197
Alignment explanation
Indices: 1--481 Score: 599
Period size: 196 Copynumber: 2.4 Consensus size: 197
* * *
1 AATTCGGTACCATGAAATATGATGGGAATGGTTGAGGCCGTAACAGCGAACCCAGTACCATGAAG
1 AATTCGGTACCATGAAATGTGATGGGAAAGGTTGAGGCCGTAATAGCGAACCCAGTACCATGAAG
* * * * *
66 ATTTGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGATACCTTAAAAGATTTGAAGGGAAAGG
66 ATTTGAAGGGAAAGGTTGAGGCCACAACGACGAACCAGATACCTTAAAAGATGTGAAGGGAAAGG
* * ** * * **
131 TTGATGCCGCAACGGTGAATTAGGTACCTTAGAAGATGTGATAGGAAAGATT-AGTCCACAACGG
131 TTGAGGCCGCAACGGCGAACCAGGTACCTCAGAAGATGTGATAGGAAAGATTGAGGCCACAACAA
*
195 TG
196 CG
* * * * *
197 AATTCGGTACCATGAAATGTGATGGAAAAGGTTGAGGCAGCAATAGCGTACCCAGTACCATAAAG
1 AATTCGGTACCATGAAATGTGATGGGAAAGGTTGAGGCCGTAATAGCGAACCCAGTACCATGAAG
* * *
262 ATTTGGAGGGAAAGGTTGAGGCCATAACGACGAACCTAG-TACCTTAAAAGATGTGACGGGAAAG
66 ATTTGAAGGGAAAGGTTGAGGCCACAACGACGAACC-AGATACCTTAAAAGATGTGAAGGGAAAG
* * * * **
326 GTTGAGGCCGCAATGGCGAACCCGGTACCTCATAAGATGTGATGGGAAAGATTGAGGCCGTAACA
130 GTTGAGGCCGCAACGGCGAACCAGGTACCTCAGAAGATGTGATAGGAAAGATTGAGGCCACAACA
391 ACG
195 ACG
* * * *
394 AA-TCTGGTACCATGAAATGTGATGGGAAAGGTTGAGACCGTAATGGCGAACCCGGTGCCATGAA
1 AATTC-GGTACCATGAAATGTGATGGGAAAGGTTGAGGCCGTAATAGCGAACCCAGTACCATGAA
*
458 GATTTTAAGGGAAAGGTTGAGGCC
65 GATTTGAAGGGAAAGGTTGAGGCC
482 GCAGCGGCAG
Statistics
Matches: 240, Mismatches: 42, Indels: 5
0.84 0.15 0.02
Matches are distributed among these distances:
196 157 0.65
197 83 0.35
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.20
Consensus pattern (197 bp):
AATTCGGTACCATGAAATGTGATGGGAAAGGTTGAGGCCGTAATAGCGAACCCAGTACCATGAAG
ATTTGAAGGGAAAGGTTGAGGCCACAACGACGAACCAGATACCTTAAAAGATGTGAAGGGAAAGG
TTGAGGCCGCAACGGCGAACCAGGTACCTCAGAAGATGTGATAGGAAAGATTGAGGCCACAACAA
CG
Found at i:395 original size:100 final size:97
Alignment explanation
Indices: 203--481 Score: 292
Period size: 98 Copynumber: 2.8 Consensus size: 97
193 GGTGAATTCG
* * * * * * *
203 GTACCATGAAATGTGATGGAAAAGGTTGAGGCAGCAATAGCGTACCCAGTACCATAAAGATTTGG
1 GTACCATAAAATGTGATGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCATAAAGATGTGG
* *
268 AGGGAAAGGTTGAGGCCATAACGACGAACCTA
66 AGGGAAAGATTGAGGCCATAACAACGAACCTA
* *
300 GTACCTTAAAAGATGTGACGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACC-TCATAAGAT
1 GTACCAT-AAA-ATGTGATGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCAT-A-AAGAT
* * *
364 GT-GATGGGAAAGATTGAGGCCGTAACAACGAATCTG
62 GTGGA-GGGAAAGATTGAGGCCATAACAACGAACCTA
* * * * * * **
400 GTACCATGAAATGTGATGGGAAAGGTTGAGACCGTAATGGCGAACCCGGTGCCATGAAGATTTTA
1 GTACCATAAAATGTGATGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCATAAAGATGTGG
*
465 AGGGAAAGGTTGAGGCC
66 AGGGAAAGATTGAGGCC
482 GCAGCGGCAG
Statistics
Matches: 151, Mismatches: 24, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
97 27 0.18
98 43 0.28
99 43 0.28
100 38 0.25
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.19
Consensus pattern (97 bp):
GTACCATAAAATGTGATGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCATAAAGATGTGG
AGGGAAAGATTGAGGCCATAACAACGAACCTA
Found at i:475 original size:246 final size:245
Alignment explanation
Indices: 24--480 Score: 544
Period size: 246 Copynumber: 1.9 Consensus size: 245
14 GAAATATGAT
* * * *
24 GGGAATGGTTGAGGCCGTAACAGCGAACCCAGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCC
1 GGGAAAGGTTGAGGCCATAACAGCGAACCCAGTACCATAAAGATGTGAAGGGAAAGGTTGAGGCC
* * * * ***
89 GCAATGGCGAACCCGATACCTTAAAAGATTTGAAGGGAAAGGTTGATGCCGCAACGGTGAATTAG
66 GCAATGGCGAACCCGATACCTCAAAAGATGTGAAGGGAAAGATTGAGGCCGCAACAACGAATTAG
* * * **
154 GTACCTTAGAAGATGTGATAGGAAAGATTAGTCCACAACGGTGAATTCGGTACCATGAAATGTGA
131 GTACCATAGAAGATGTGATAGGAAAGATTAGACCACAACGGCGAACCCGGTACCATGAAATGTGA
*
219 TGGAAAAGGTTGAGGCAGCAATAGCGTACCCAGTACCATAAAGATTTGGA
196 AGGAAAAGGTTGAGGCAGCAATAGCGTACCCAGTACCATAAAGATTTGGA
* * *
269 GGGAAAGGTTGAGGCCATAAC-GACGAACCTAGTACCTTAAAAGATGTGACGGGAAAGGTTGAGG
1 GGGAAAGGTTGAGGCCATAACAG-CGAACCCAGTACCAT-AAAGATGTGAAGGGAAAGGTTGAGG
* * * *
333 CCGCAATGGCGAACCCGGTACCTCATAAGATGTGATGGGAAAGATTGAGGCCGTAACAACGAATC
64 CCGCAATGGCGAACCCGATACCTCAAAAGATGTGAAGGGAAAGATTGAGGCCGCAACAACGAAT-
* * ** * *
398 T-GGTACCAT-GAA-ATGTGATGGGAAAGGTTGAGACCGTAATGGCGAACCCGGTGCCATGAAGA
128 TAGGTACCATAGAAGATGTGATAGGAAAGATT-AGACCACAACGGCGAACCCGGTACCATGAA-A
* * *
460 TTTTAAGGGAAAGGTTGAGGC
191 TGTGAAGGAAAAGGTTGAGGC
481 CGCAGCGGCA
Statistics
Matches: 174, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
244 16 0.09
245 57 0.33
246 100 0.57
247 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (245 bp):
GGGAAAGGTTGAGGCCATAACAGCGAACCCAGTACCATAAAGATGTGAAGGGAAAGGTTGAGGCC
GCAATGGCGAACCCGATACCTCAAAAGATGTGAAGGGAAAGATTGAGGCCGCAACAACGAATTAG
GTACCATAGAAGATGTGATAGGAAAGATTAGACCACAACGGCGAACCCGGTACCATGAAATGTGA
AGGAAAAGGTTGAGGCAGCAATAGCGTACCCAGTACCATAAAGATTTGGA
Found at i:809 original size:39 final size:39
Alignment explanation
Indices: 762--1298 Score: 263
Period size: 39 Copynumber: 13.7 Consensus size: 39
752 TTGAAGATTC
* * *
762 CGATCTCTTACCTCGAGCCTGGGGTAGATTACAACCATT
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATT
* * * **
801 CGATCTCTTACCCCGAGCCTGGGGAAGATCACCATCAGC
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATT
* * * * *
840 CAATCTCATACCCCGAGCCTGGGGTAGATTACAACCGTT
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATT
* * ** * ** * **
879 TGATCTCTTACCCCGAGCTTAAGGCAGATCACCGTTAGC
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATT
* * * * * *
918 CAATCTCTTACCTCGAGCTTGGGGTAGATTGCAA-CTGTT
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATC-ATT
* * * ** **
957 CGATCTCTTACCTCGAGCCTAGGGCAGATCACCGTCAAC
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATT
* * * ****
996 CAATCTCTTACCCCGAGCCTGGGGTAAATTGTTGTCATT
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATT
* * * * * **
1035 AGATCTCTTACCCCGACCCTGGGGCAAATCACCATCAGC
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATT
* * * * *
1074 CAATCTCTTACCCCGAGCCTCGAGCAGATTGC-AGCAATT
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATC-ATT
* * **
1113 CGATCTCTTACCCCAAGCCTGGGGCAGATCATC-ATCAGC
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTA-CAATCATT
* * * * * *
1152 CAATCTATTACCCCGA-CCTTGGGGCAAATTGCAGTCACT
1 CGATCTCTTACCCCGAGCC-TGGGGCAGATTACAATCATT
* * * * **
1191 CGATCTCTTACCTCGAGCCTAGAGGCAGATCACCATCAGC
1 CGATCTCTTACCCCGAGCCT-GGGGCAGATTACAATCATT
* * * * * ** *
1231 CAATCTCTTACCTCTAGCTTGGGCCAGATTGTAACCATT
1 CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATT
* * *
1270 CGATCTTTTACCTCGAGCATGGGGCAGAT
1 CGATCTCTTACCCCGAGCCTGGGGCAGAT
1299 CATCATCAGC
Statistics
Matches: 355, Mismatches: 135, Indels: 16
0.70 0.27 0.03
Matches are distributed among these distances:
38 5 0.01
39 316 0.89
40 34 0.10
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (39 bp):
CGATCTCTTACCCCGAGCCTGGGGCAGATTACAATCATT
Found at i:860 original size:78 final size:78
Alignment explanation
Indices: 764--1320 Score: 603
Period size: 78 Copynumber: 7.1 Consensus size: 78
754 GAAGATTCCG
* * *
764 ATCTCTTACCTCGAGCCTGGGGTAGATTACAACCATTCGATCTCTTACCCCGAGCCTGGGGAAGA
1 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGCAGA
829 TCACCATCAGCCA
66 TCACCATCAGCCA
* * * * * **
842 ATCTCATACCCCGAGCCTGGGGTAGATTACAACCGTTTGATCTCTTACCCCGAGCTTAAGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGCAGA
* *
907 TCACCGTTAGCCA
66 TCACCATCAGCCA
* * ** * *
920 ATCTCTTACCTCGAGCTTGGGGTAGATTGCAACTGTTCGATCTCTTACCTCGAGCCTAGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGCAGA
* *
985 TCACCGTCAACCA
66 TCACCATCAGCCA
* **** * * *
998 ATCTCTTACCCCGAGCCTGGGGTAAATTGTTGTCATTAGATCTCTTACCCCGACCCTGGGGCAAA
1 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGCAGA
1063 TCACCATCAGCCA
66 TCACCATCAGCCA
* * * * * *
1076 ATCTCTTACCCCGAGCCTCGAGCAGATTGCAGCAATTCGATCTCTTACCCCAAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGCAGA
*
1141 TCATCATCAGCCA
66 TCACCATCAGCCA
* * * ** * * *
1154 ATCTATTACCCCGA-CCTTGGGGCAAATTGCAGTCACTCGATCTCTTACCTCGAGCCTAGAGGCA
1 ATCTCTTACCCCGAGCC-TGGGGTAGATTGCAACCATTCGATCTCTTACCCCGAGCCT-GGGGCA
1218 GATCACCATCAGCCA
64 GATCACCATCAGCCA
* * * ** * * * *
1233 ATCTCTTACCTCTAGCTTGGGCCAGATTGTAACCATTCGATCTTTTACCTCGAGCATGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGCAGA
*
1298 TCATCATCAGCCA
66 TCACCATCAGCCA
*
1311 ACCTCTTACC
1 ATCTCTTACC
1321 TCGATCATGA
Statistics
Matches: 400, Mismatches: 76, Indels: 6
0.83 0.16 0.01
Matches are distributed among these distances:
77 2 0.00
78 335 0.84
79 62 0.16
80 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGCAGA
TCACCATCAGCCA
Found at i:1080 original size:117 final size:117
Alignment explanation
Indices: 959--1324 Score: 317
Period size: 117 Copynumber: 3.1 Consensus size: 117
949 CAACTGTTCG
* * *
959 ATCTCTTACCTCGAGCCTAGGGCAGATCACCGTCAACCAATCTCTTACCCCGAGCCTGGGGTAAA
1 ATCTCTTACCTCGAGCCTAGGGCAGATCACCGTCAACCAATCTCTTACCCCAAGCCTGGGGCAGA
** * *
1024 TTGTTGTCATTAGATCTCTTACCCCGACCCTGGGGCAAATCACCATCAGCCA
66 TTGTAATCATTAGATCTATTACCCCGACCATGGGGCAAATCACCATCAGCCA
* * * ** * * *
1076 ATCTCTTACCCCGAGCCTCGAGCAGATTGCAG-CAATTCGATCTCTTACCCCAAGCCTGGGGCAG
1 ATCTCTTACCTCGAGCCTAGGGCAGATCACCGTCAA-CCAATCTCTTACCCCAAGCCTGGGGCAG
** * ** * ** *
1140 ATCATCATCAGCCA-ATCTATTACCCCGACCTTGGGGCAAAT-TGCAGTCA-CTCG
65 ATTGTAATCA-TTAGATCTATTACCCCGACCATGGGGCAAATCACCA-TCAGC-CA
* * * * * *
1193 ATCTCTTACCTCGAGCCTAGAGGCAGATCACCATCAGCCAATCTCTTACCTCTAGCTTGGGCCAG
1 ATCTCTTACCTCGAGCCTAG-GGCAGATCACCGTCAACCAATCTCTTACCCCAAGCCTGGGGCAG
* * * * * * *
1258 ATTGTAACCATTCGATCTTTTACCTCGAGCATGGGGCAGATCATCATCAGCCA
65 ATTGTAATCATTAGATCTATTACCCCGACCATGGGGCAAATCACCATCAGCCA
*
1311 ACCTCTTACCTCGA
1 ATCTCTTACCTCGA
1325 TCATGAGGCA
Statistics
Matches: 188, Mismatches: 52, Indels: 17
0.73 0.20 0.07
Matches are distributed among these distances:
116 6 0.03
117 102 0.54
118 75 0.40
119 5 0.03
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.25
Consensus pattern (117 bp):
ATCTCTTACCTCGAGCCTAGGGCAGATCACCGTCAACCAATCTCTTACCCCAAGCCTGGGGCAGA
TTGTAATCATTAGATCTATTACCCCGACCATGGGGCAAATCACCATCAGCCA
Found at i:1783 original size:17 final size:17
Alignment explanation
Indices: 1761--1845 Score: 98
Period size: 17 Copynumber: 5.0 Consensus size: 17
1751 TGGACCTATT
*
1761 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
1778 TTTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
1795 GTTTCAATTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
1812 TTTTGAATTTAAATTCA
1 TTTTAAATTTAAATTTA
**
1829 TTACAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
1846 ATTAAAAATT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:1805 original size:23 final size:23
Alignment explanation
Indices: 1762--1858 Score: 58
Period size: 23 Copynumber: 4.3 Consensus size: 23
1752 GGACCTATTT
* *
1762 TTTAAATTTTAATTTATTTTAAG
1 TTTAAATTTTAATTTAATTTAAA
*
1785 TTTAAA-TTTAGTTTCAATTTAAA
1 TTTAAATTTTAATTT-AATTTAAA
* *
1808 TTT--ATTTTGAATTTAAATT-CA
1 TTTAAATTTT-AATTTAATTTAAA
* * *
1829 TTACAAATTTAAATTTAATTAAAA
1 TT-TAAATTTTAATTTAATTTAAA
*
1853 ATTAAA
1 TTTAAA
1859 AAAGAGCGCA
Statistics
Matches: 54, Mismatches: 13, Indels: 14
0.67 0.16 0.17
Matches are distributed among these distances:
21 4 0.07
22 14 0.26
23 30 0.56
24 6 0.11
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (23 bp):
TTTAAATTTTAATTTAATTTAAA
Found at i:1854 original size:18 final size:17
Alignment explanation
Indices: 1817--1855 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1807 ATTTATTTTG
* *
1817 AATTTAAATTCATTACA
1 AATTTAAATTAATTAAA
1834 AATTTAAATTTAATTAAA
1 AATTTAAA-TTAATTAAA
1852 AATT
1 AATT
1856 AAAAAAGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAATTAATTAAA
Done.