Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010817.1 Kokia drynarioides strain JFW-HI SEQ_125784, 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, 963
Length: 1605
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:266 original size:39 final size:39
Alignment explanation
Indices: 168--254 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
158 TAATCTACCC
* *
168 CATGATCGGGGTAAGAGATTGAATGGCTGTGATCTGTCT
1 CATGATCGGGGTAAGAGATCGAATGGCTGTGATCTGCCT
* *
207 CATGGTCGGGGTAAGAGATCGAGTGGCTGTGATCTGCCT
1 CATGATCGGGGTAAGAGATCGAATGGCTGTGATCTGCCT
246 CATGATCGG
1 CATGATCGG
255 TATAAAAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.21, C:0.16, G:0.36, T:0.28
Consensus pattern (39 bp):
CATGATCGGGGTAAGAGATCGAATGGCTGTGATCTGCCT
Found at i:359 original size:39 final size:39
Alignment explanation
Indices: 168--348 Score: 134
Period size: 39 Copynumber: 4.6 Consensus size: 39
158 TAATCTACCC
* *
168 CATGATCGGGGTAAGAGATTGAATGGCTGTGATCTGTCT
1 CATGATCGGGGTAAGAGATTGAATGGCTGTGATTTGCCT
* * * *
207 CATGGTCGGGGTAAGAGATCGAGTGGCTGTGATCTGCCT
1 CATGATCGGGGTAAGAGATTGAATGGCTGTGATTTGCCT
** * * * * ** * *
246 CATGATCGGTATAAAAGATCGGATGGTTGCAATTTTCCC
1 CATGATCGGGGTAAGAGATTGAATGGCTGTGATTTGCCT
** *
285 CTATTG-TC-GGGTAAGAGATTGGCT-GATAGTGATTTGCCT
1 C-A-TGATCGGGGTAAGAGATTGAATGGCT-GTGATTTGCCT
*
324 CATGATCGGGGTAAAAGATTGAATG
1 CATGATCGGGGTAAGAGATTGAATG
349 ACTGCAATTT
Statistics
Matches: 107, Mismatches: 29, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
37 2 0.02
38 5 0.05
39 95 0.89
40 3 0.03
41 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.30
Consensus pattern (39 bp):
CATGATCGGGGTAAGAGATTGAATGGCTGTGATTTGCCT
Found at i:474 original size:37 final size:38
Alignment explanation
Indices: 374--486 Score: 104
Period size: 37 Copynumber: 2.9 Consensus size: 38
364 AGGCTCAGGA
* * * *
374 TAAGAGATTGACTAATGGTGATCTACCTCAGGCTCGAGG
1 TAAGAGATTGGCTGATGGTGATCTGCC-CAGACTCGAGG
* * * *
413 TAAAAGATCGGATGACT-GTAATCTGCCC-GACTCGAGG
1 TAAGAGATTGGCTGA-TGGTGATCTGCCCAGACTCGAGG
*
450 TAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGA
1 TAAGAGATTGGCTGATGGTGATCTGCCC-AGACTCGA
487 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
36 1 0.02
37 30 0.53
38 1 0.02
39 24 0.42
40 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (38 bp):
TAAGAGATTGGCTGATGGTGATCTGCCCAGACTCGAGG
Found at i:483 original size:76 final size:77
Alignment explanation
Indices: 294--486 Score: 212
Period size: 78 Copynumber: 2.5 Consensus size: 77
284 CCTATTGTCG
* * * * * * *
294 GGTAAGAGATTGGCTGATAGTGATTTGCCTCATGATCGGGGTAAAAGATTGAATGACTGCAATTT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGATCGAATGACTGCAATCT
*
359 GTCCTAGGCTCA
66 GTCCTAGACTCA
* * * * *
371 GGATAAGAGATTGACTAATGGTGATCTACCTCAGGCTCGAGGTAAAAGATCGGATGACTGTAATC
1 GG-TAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGATCGAATGACTGCAATC
*
436 TG-CC-CGACTCGA
65 TGTCCTAGACTC-A
448 GGTAAGAGATTGGCTGATGGTGATCTGCC-CTAGGCTCGA
1 GGTAAGAGATTGGCTGATGGTGATCTGCCTC-AGGCTCGA
487 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
75 1 0.01
76 36 0.38
77 7 0.07
78 52 0.54
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (77 bp):
GGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGATCGAATGACTGCAATCT
GTCCTAGACTCA
Found at i:607 original size:39 final size:39
Alignment explanation
Indices: 564--684 Score: 140
Period size: 39 Copynumber: 3.1 Consensus size: 39
554 AATGACTGCA
* *
564 ATCTGCCCTAGGCTTAGGGTAAGAGATTAGTTGATGGTG
1 ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
* * * *
603 ATCTGCCCCAAGCTCGGGGTAAAAGA-TCG--GATGGCTG
1 ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGG-TG
640 CAATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
1 --ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
681 ATCT
1 ATCT
685 ACCTCAGGCT
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
36 5 0.08
37 2 0.03
38 2 0.03
39 48 0.73
40 2 0.03
41 2 0.03
42 5 0.08
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.27
Consensus pattern (39 bp):
ATCTGCCCTAAGCTTGGGGTAAGAGATTAGTTGATGGTG
Found at i:641 original size:78 final size:78
Alignment explanation
Indices: 503--719 Score: 317
Period size: 78 Copynumber: 2.8 Consensus size: 78
493 NNNNACTCGA
* * * ** *
503 GGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGAAGTAAATGATCGAATGACTGCAATCT
1 GGTAAGAGATTAGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTGCAATCT
*
568 GCCCTAGGCTTAG
66 GCCCTAAGCTTAG
* * *
581 GGTAAGAGATTAGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT
1 GGTAAGAGATTAGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTGCAATCT
*
646 GCCCTAAGCTTGG
66 GCCCTAAGCTTAG
* *
659 GGTAAGAGATTAGTTGATGGTGATCTACCTCAGGCTCGGGGTAAAAGATCGAATGACTGCA
1 GGTAAGAGATTAGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTGCA
720 NNNNNGATGG
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 123 1.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (78 bp):
GGTAAGAGATTAGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTGCAATCT
GCCCTAAGCTTAG
Found at i:700 original size:39 final size:38
Alignment explanation
Indices: 580--707 Score: 127
Period size: 39 Copynumber: 3.3 Consensus size: 38
570 CCTAGGCTTA
*
580 GGGTAAGAGATTAGTTGATGGTGATCTGCCCCAAGCTCG
1 GGGTAAAAGATTAGTTGATGGTGATCTG-CCCAAGCTCG
* *
619 GGGTAAAAGA-TCG--GATGGCTGCAATCTGCCCTAAGCTTG
1 GGGTAAAAGATTAGTTGATGG-TG--ATCTGCCC-AAGCTCG
* * *
658 GGGTAAGAGATTAGTTGATGGTGATCTACCTCAGGCTCG
1 GGGTAAAAGATTAGTTGATGGTGATCTGCC-CAAGCTCG
697 GGGTAAAAGAT
1 GGGTAAAAGAT
708 CGAATGACTG
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
36 5 0.07
37 2 0.03
38 5 0.07
39 50 0.69
40 3 0.04
41 2 0.03
42 5 0.07
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (38 bp):
GGGTAAAAGATTAGTTGATGGTGATCTGCCCAAGCTCG
Found at i:830 original size:129 final size:124
Alignment explanation
Indices: 596--848 Score: 319
Period size: 129 Copynumber: 2.0 Consensus size: 124
586 GAGATTAGTT
*
596 GATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAAGCTTGGGG
1 GATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAAGCTCGGGG
* * * *
661 TAAGAGATTAGTTGATGGTGATCTACCTCAGGCTCGGGGTAAAAGATCGAATGACTGCA
66 TAAGAGATTAGCTGATGGTGATCTACCCCAAGCTCAGGGTAAAAGATCGAATGACTGCA
** * * * *
720 NNNNNGATGGTGATCTGCCTTAGGCTCGGGGTAAAAGATCGGATGGCTTCAATCTATCCC-AGGC
1 -----GATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-GCCCTAAGC
* * *
784 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGAATGGCTGCA
60 TCGGGGTAAGAGATTAGCTGATGGTGATCTACCCCAAGCTCAGGGTAAAAGATCGAATGACTGCA
849 ATCTGCGATT
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
129 106 0.97
130 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.23
Consensus pattern (124 bp):
GATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAAGCTCGGGG
TAAGAGATTAGCTGATGGTGATCTACCCCAAGCTCAGGGTAAAAGATCGAATGACTGCA
Found at i:1324 original size:49 final size:49
Alignment explanation
Indices: 1182--1605 Score: 236
Period size: 49 Copynumber: 8.7 Consensus size: 49
1172 TAAGACTCGT
* * * *
1182 CGTTGCGGCCTCAACCTTTCCCATCATAT-TTCATGGTA-TCAGATTCGT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACT-GGGTTCGC
** * * ** * * *
1230 TATTGCGGCCTCAATCATTGTCATC-CATCTTTTAAGGT-GTCGGGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATC-TTCATGGTACT-GGGTTCGC
* * * * *
1279 CATTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTTGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACTGGGTTCGC
* * * * * * ** * **
1328 CATTGCTGCCTCAACTTTTTCAATCGCATCTTCATGGTACCAGATTTAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACTGGGTTCGC
* * *
1377 CGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTATTGGGTTTGC
1 CGTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-ATGGTACTGGGTTCGC
* * * * * *
1427 CGTTGTGGCCTCAACCTTTCCCTTTAAATCTTCATGGTA-TCGAGTTCGT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACT-GGGTTCGC
* * * ** *
1476 CATTACGGTCTCAACCTTTCCCATCACAT-TTCATGGTA-TCGAATTCAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACT-GGGTTCGC
* * * *
1524 CGTTGCGGCCTTAATCTTTCCCATCACATCTTTTAAGGTAC-GAGGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATC-TTCATGGTACTG-GGTTCGC
* * * *
1574 CGTTGTGGCCTCAATCTTTCCCTTCAAATCTT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTT
Statistics
Matches: 283, Mismatches: 80, Indels: 25
0.73 0.21 0.06
Matches are distributed among these distances:
47 2 0.01
48 60 0.21
49 143 0.51
50 78 0.28
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.36
Consensus pattern (49 bp):
CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACTGGGTTCGC
Found at i:1497 original size:99 final size:98
Alignment explanation
Indices: 1273--1513 Score: 231
Period size: 99 Copynumber: 2.4 Consensus size: 98
1263 AAGGTGTCGG
* * *
1273 GTTCGCCATTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTTGCCATTGCTGCC
1 GTTCG-CATTACGGCCTCAACCTTTCCCATCACATCTTCAAGGTACTGGGTTTGCCATTGCTGCC
* * **
1338 TCAACTTTTTCAATCGCATCTTCATGGTACCAGA
65 TCAACCTTTCCAATCAAATCTTCATGGTACCAGA
* * * * *
1372 TTTAC-CGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTATTGGGTTTGCCGTTG-TG
1 GTT-CGCATTACGGCCTCAA-CCTTTCCCATCACATCTTC-AAGGTACTGGGTTTGCCATTGCT-
** * *
1434 GCCTCAACCTTTCCCTTTAAATCTTCATGGTATC-GA
62 GCCTCAACCTTTCCAATCAAATCTTCATGGTACCAGA
* *
1470 GTTCGTCATTACGGTCTCAACCTTTCCCATCACAT-TTCATGGTA
1 GTTCG-CATTACGGCCTCAACCTTTCCCATCACATCTTCAAGGTA
1514 TCGAATTCAC
Statistics
Matches: 114, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
97 6 0.05
98 36 0.32
99 71 0.62
100 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (98 bp):
GTTCGCATTACGGCCTCAACCTTTCCCATCACATCTTCAAGGTACTGGGTTTGCCATTGCTGCCT
CAACCTTTCCAATCAAATCTTCATGGTACCAGA
Found at i:1563 original size:147 final size:147
Alignment explanation
Indices: 1187--1605 Score: 495
Period size: 147 Copynumber: 2.9 Consensus size: 147
1177 CTCGTCGTTG
* **** **
1187 CGGCCTCAACCTTTCCCATCATATTTCATGGTATCAGATTCGTTATTGCGGCCTCAATCATTGTC
1 CGGCCTCAACCTTTCCCATCACATTTCATGGTATCAGATTCACCGTTGCGGCCTCAATCATTCCC
* * **
1252 ATC-CATCTTTTAAGGTGTCGGGTTCGCCATTACGGCCTCAACCTTTCCCTTCAAATCTTCATGG
66 ATCACATCTTTTAAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCAAATCTTCATGG
* * *
1316 TACTGGGTTTGCCATTG
131 TACTGAGTTCGCCATTA
* * * * * * * *
1333 CTGCCTCAACTTTTTCAATCGCATCTTCATGGTACCAGATTTACCGTTGCGGCCTCAATCCTTCC
1 CGGCCTCAACCTTTCCCATCACAT-TTCATGGTATCAGATTCACCGTTGCGGCCTCAATCATTCC
* * * *
1398 CATCACATCTTCTAAGGTATTGGGTTTGCCGTTGTGGCCTCAACCTTTCCCTTTAAATCTTCATG
65 CATCACATCTTTTAAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCAAATCTTCATG
*
1463 GTA-TCGAGTTCGTCATTA
130 GTACT-GAGTTCGCCATTA
* * *
1481 CGGTCTCAACCTTTCCCATCACATTTCATGGTATC-GAATTCACCGTTGCGGCCTTAATCTTTCC
1 CGGCCTCAACCTTTCCCATCACATTTCATGGTATCAG-ATTCACCGTTGCGGCCTCAATCATTCC
*
1545 CATCACATCTTTTAAGGTA-CGAGGTTCGCCGTTGTGGCCTCAATCTTTCCCTTCAAATCTT
65 CATCACATCTTTTAAGGTATCG-GGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCAAATCTT
Statistics
Matches: 226, Mismatches: 42, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
146 20 0.09
147 124 0.55
148 82 0.36
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (147 bp):
CGGCCTCAACCTTTCCCATCACATTTCATGGTATCAGATTCACCGTTGCGGCCTCAATCATTCCC
ATCACATCTTTTAAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCAAATCTTCATGG
TACTGAGTTCGCCATTA
Done.