Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012364.1 Kokia drynarioides strain JFW-HI SEQ_127368, 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: 4278
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.26
Warning! 167 characters in sequence are not A, C, G, or T
Found at i:3380 original size:43 final size:43
Alignment explanation
Indices: 3251--3380 Score: 97
Period size: 43 Copynumber: 3.0 Consensus size: 43
3241 ATGGTGGTGT
* * *
3251 GGGACCATCGGGAAGTATCGGAACCATGGTGCCTTCGATGTGA
1 GGGACCATCGAGAAGTATCGGTACCATGGTGCCTTCGATGTGC
** ** * * * *
3294 GGGTGCATCGA-ACACCATTGGTAAC-TGAG-GCCGAT-GGTGGTGC
1 GGGACCATCGAGA-AGTATCGGTACCATG-GTGCC-TTCGAT-GTGC
3337 GGGACCATCGAGAAGTATCGGTACCATGGTGCCTTCGATGTGC
1 GGGACCATCGAGAAGTATCGGTACCATGGTGCCTTCGATGTGC
3380 G
1 G
3381 ATAGCATCGA
Statistics
Matches: 60, Mismatches: 19, Indels: 16
0.63 0.20 0.17
Matches are distributed among these distances:
42 8 0.13
43 44 0.73
44 8 0.13
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.22
Consensus pattern (43 bp):
GGGACCATCGAGAAGTATCGGTACCATGGTGCCTTCGATGTGC
Found at i:3519 original size:86 final size:85
Alignment explanation
Indices: 3127--3528 Score: 448
Period size: 86 Copynumber: 4.7 Consensus size: 85
3117 TGTGCTGGAT
* * * * *
3127 CATCGGACACCATCGGTAGCTTAGGTCGATGGTGGTACGGGACCATCGAGAATCATCGGTACCTT
1 CATC-GACACCATCGGTAACTTAGGTCGATGGTGGTGCGGGACCATCGGGAAGCATCGGTACCAT
* *
3192 GGTGCC-TCAAATGTGCGGGAG
65 GGTGCCTTC-GATGTGCGAGAG
* * * * * *
3213 TATCGGACACCATCGGTAACTAAGG-CAAATGGTGGTGTGGGACCATCGGGAAGTATCGGAACCA
1 CATC-GACACCATCGGTAACTTAGGTC-GATGGTGGTGCGGGACCATCGGGAAGCATCGGTACCA
* * *
3277 TGGTGCCTTCGATGTGAGGGTG
64 TGGTGCCTTCGATGTGCGAGAG
* * * * *
3299 CATCGAACACCATTGGTAACTGAGGCCGATGGTGGTGCGGGACCATCGAGAAGTATCGGTACCAT
1 CATCG-ACACCATCGGTAACTTAGGTCGATGGTGGTGCGGGACCATCGGGAAGCATCGGTACCAT
*
3364 GGTGCCTTCGATGTGCGATAG
65 GGTGCCTTCGATGTGCGAGAG
* * * ** *
3385 CATCGAACACCATCGGTAACATAGGTCGATGGTGATGCGGGACAATCGGGATCCATCGGTACCTT
1 CATCG-ACACCATCGGTAACTTAGGTCGATGGTGGTGCGGGACCATCGGGAAGCATCGGTACCAT
*
3450 GGTGCCTTGGATGTGCGAGAG
65 GGTGCCTTCGATGTGCGAGAG
* *
3471 CATCAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGGGTCTATCGGGAAGCATCG
1 CATC-GACACCATCGGTAACTTAGGTCGATGGTGGTGCGGGACCATCGGGAAGCATCG
3529 AACACCATCG
Statistics
Matches: 267, Mismatches: 44, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
85 2 0.01
86 261 0.98
87 4 0.01
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (85 bp):
CATCGACACCATCGGTAACTTAGGTCGATGGTGGTGCGGGACCATCGGGAAGCATCGGTACCATG
GTGCCTTCGATGTGCGAGAG
Found at i:3536 original size:139 final size:139
Alignment explanation
Indices: 3383--3660 Score: 405
Period size: 139 Copynumber: 2.0 Consensus size: 139
3373 GATGTGCGAT
** ** *
3383 AGCATCGAACACCATCGGTAAC-ATAGGTCGATGGTGATGCGGGACAATCGGGATCCATCGGTAC
1 AGCATCGAACACCATCGAAAACTA-AGGTCGATGGTGATGCAAGACAATCGGGAACCATCGGTAC
* *
3447 CTTGGTGCCTTGGATGTGCGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGGG
65 CTTGGTACCTTGGATGTGCGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGATGGTGCGGG
* *
3512 TCTATCGGGA
130 ACCATCGGGA
* * * *
3522 AGCATCGAACACCATCGAAAACTAAGGTCGATGGTGGTGTAAGACCATCGGGAAGCATCGGTACC
1 AGCATCGAACACCATCGAAAACTAAGGTCGATGGTGATGCAAGACAATCGGGAACCATCGGTACC
* *
3587 TTGGTACCTTGGATGTGCGAGAGCATCGGACACTATCGGTAACTTAGGTCGATGATGGTGCGGGA
66 TTGGTACCTTGGATGTGCGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGATGGTGCGGGA
3652 CCATCGGGA
131 CCATCGGGA
3661 TCCATCGGTA
Statistics
Matches: 123, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
139 122 0.99
140 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (139 bp):
AGCATCGAACACCATCGAAAACTAAGGTCGATGGTGATGCAAGACAATCGGGAACCATCGGTACC
TTGGTACCTTGGATGTGCGAGAGCATCAGACACCATCGGTAACTTAGGTCGATGATGGTGCGGGA
CCATCGGGA
Found at i:3556 original size:225 final size:225
Alignment explanation
Indices: 3298--3758 Score: 663
Period size: 225 Copynumber: 2.1 Consensus size: 225
3288 ATGTGAGGGT
* ** * ** *
3298 GCATCGAACACCATTGGTAACTGAGGCCGATGGTGGTGCGGGACCATCGAGAAGTATCGGTACCA
1 GCATCGAACACCATCGAAAACTAAGGCCGATGGTGGTGCAAGACCATCGAGAAGCATCGGTACCA
* * *
3363 TGGTGCCTTCGATGTGCGATAGCATCGAACACCATCGGTAACATAGGTCGATGGTGATGCGGGAC
66 TGGTACCTTCGATGTGCGAGAGCATCGAACACCATCGGTAACATAGGTCGATGATGATGCGGGAC
* *
3428 AATCGGGATCCATCGGTACCTTGGTGCCTTGGATGTGCGAGAGCATCAGACACCATCGGTAACTT
131 AATCGGGATCCATCGGTACCTTGGTACCTTGGATGTGCGAGAGCATCAGACACCATCGATAACTT
* * * *
3493 AGGTCGATGGTGGTGCGGGTCTATCGGGAA
196 AGGCCGATGGTGGTGCCGGACCATCGGGAA
* * * *
3523 GCATCGAACACCATCGAAAACTAAGGTCGATGGTGGTGTAAGACCATCGGGAAGCATCGGTACCT
1 GCATCGAACACCATCGAAAACTAAGGCCGATGGTGGTGCAAGACCATCGAGAAGCATCGGTACCA
* * * * *
3588 TGGTACCTTGGATGTGCGAGAGCATCGGACACTATCGGTAACTTAGGTCGATGATGGTGCGGGAC
66 TGGTACCTTCGATGTGCGAGAGCATCGAACACCATCGGTAACATAGGTCGATGATGATGCGGGAC
* * *
3653 CATCGGGATCCATCGGTACCTTGGTACCTTGGATGTGCGAGAGCATCGGACACCCTCGATAACTT
131 AATCGGGATCCATCGGTACCTTGGTACCTTGGATGTGCGAGAGCATCAGACACCATCGATAACTT
3718 AGGCCGATGGTGGTGCCGGACCATCGGGAA
196 AGGCCGATGGTGGTGCCGGACCATCGGGAA
3748 GCATCG-ACACC
1 GCATCGAACACC
3759 TTGGTGCCTC
Statistics
Matches: 208, Mismatches: 28, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
224 5 0.02
225 203 0.98
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (225 bp):
GCATCGAACACCATCGAAAACTAAGGCCGATGGTGGTGCAAGACCATCGAGAAGCATCGGTACCA
TGGTACCTTCGATGTGCGAGAGCATCGAACACCATCGGTAACATAGGTCGATGATGATGCGGGAC
AATCGGGATCCATCGGTACCTTGGTACCTTGGATGTGCGAGAGCATCAGACACCATCGATAACTT
AGGCCGATGGTGGTGCCGGACCATCGGGAA
Found at i:3572 original size:53 final size:54
Alignment explanation
Indices: 3469--3581 Score: 140
Period size: 53 Copynumber: 2.1 Consensus size: 54
3459 GATGTGCGAG
** * ** * *
3469 AGCATC-AGACACCATCGGTAACTTAGGTCGATGGTGGTGCGGGTCTATCGGGA
1 AGCATCGAGACACCATCGAAAACTAAGGTCGATGGTGGTGCAAGACCATCGGGA
*
3522 AGCATCGA-ACACCATCGAAAACTAAGGTCGATGGTGGTGTAAGACCATCGGGA
1 AGCATCGAGACACCATCGAAAACTAAGGTCGATGGTGGTGCAAGACCATCGGGA
3575 AGCATCG
1 AGCATCG
3582 GTACCTTGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 50 0.98
54 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.19
Consensus pattern (54 bp):
AGCATCGAGACACCATCGAAAACTAAGGTCGATGGTGGTGCAAGACCATCGGGA
Found at i:3646 original size:86 final size:86
Alignment explanation
Indices: 3522--3966 Score: 495
Period size: 86 Copynumber: 5.2 Consensus size: 86
3512 TCTATCGGGA
* * * * *** *
3522 AGCATCGAACACCATCGAAAACTAAGGTCGATGGTGGTGTAAGACCATCGGGAAGCATCGGTACC
1 AGCATCGGACACCATCGATAACTTAGGTCGATGATGGTGCGGGACCATCGGGAAGCATCGGCACC
*
3587 TTGGTACCTTGGATGTGCGAG
66 TTGGTGCCTTGGATGTGCGAG
* * ** *
3608 AGCATCGGACACTATCGGTAACTTAGGTCGATGATGGTGCGGGACCATCGGGATCCATCGGTACC
1 AGCATCGGACACCATCGATAACTTAGGTCGATGATGGTGCGGGACCATCGGGAAGCATCGGCACC
*
3673 TTGGTACCTTGGATGTGCGAG
66 TTGGTGCCTTGGATGTGCGAG
* * * * *
3694 AGCATCGGACACCCTCGATAACTTAGGCCGATGGTGGTGCCGGACCATCGGGAAGCATCGACACC
1 AGCATCGGACACCATCGATAACTTAGGTCGATGATGGTGCGGGACCATCGGGAAGCATCGGCACC
*
3759 TTGGTGCCTCGGATGTATG-GA-
66 TTGGTGCCTTGGATG--TGCGAG
* * * *
3780 AGCATCGGACACCATCGACAACTAAGG-CTGATGATAGTGCGGGACCATCGGGAAGTATCGGCAC
1 AGCATCGGACACCATCGATAACTTAGGTC-GATGATGGTGCGGGACCATCGGGAAGCATCGGCAC
* *
3844 CATGGTGCCTTCGATGTGC-AGG
65 CTTGGTGCCTTGGATGTGCGA-G
* ** *
3866 AGCATCGGACATCATCGGGAACTTAGGTCGATGGA-GGTGCGGGACCATCGGAAAGCATCGGCAC
1 AGCATCGGACACCATCGATAACTTAGGTCGAT-GATGGTGCGGGACCATCGGGAAGCATCGGCAC
* *
3930 CTTGGTGCCTTGCATGTGCGGG
65 CTTGGTGCCTTGGATGTGCGAG
* *
3952 AGCATGGGATACCAT
1 AGCATCGGACACCAT
3967 TGGCCCAAAA
Statistics
Matches: 302, Mismatches: 48, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
84 3 0.01
85 1 0.00
86 291 0.96
87 5 0.02
88 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (86 bp):
AGCATCGGACACCATCGATAACTTAGGTCGATGATGGTGCGGGACCATCGGGAAGCATCGGCACC
TTGGTGCCTTGGATGTGCGAG
Found at i:3822 original size:311 final size:311
Alignment explanation
Indices: 3214--3839 Score: 738
Period size: 311 Copynumber: 2.0 Consensus size: 311
3204 GTGCGGGAGT
* ** ** *
3214 ATCGGACACCATCGGTAACTAAGGCAAATGGTGGTGTGGGACCATCGGGAAGTATCGGAACCATG
1 ATCGAACACCATCGAAAACTAAGGCAAATGGTGGTGTAAGACCATCGGGAAGCATCGGAACCATG
* * * * *
3279 GTGCCTTCGATGTGAGGGTGCATCGAACACCATTGGTAACTGAGGCCGATGGTGGTGCGGGACCA
66 GTACCTTCGATGTGAGAGAGCATCGAACACCATCGGTAACTGAGGCCGATGATGGTGCGGGACCA
** * * *
3344 TCGAGAAGTATCGGTACCATGGTGCCTTCGATGTGCGATAGCATCGAACACCATCGGTAACATAG
131 TCGAGAACCATCGGTACCATGGTACCTTCGATGTGCGAGAGCATCGAACACCATCGATAACATAG
* * * ** *
3409 GTCGATGGTGATGCGGGACAATCGGGATCCATCGGTACCTTGGTGCCTTGGATGTGCGAGAGCAT
196 GCCGATGGTGATGCCGGACAATCGGGAACCATCGACACCTTGGTGCCTCGGATGTGCGAGAGCAT
** * * * * *
3474 CAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGGGTCTATCGGGAAGC
261 CAGACACCATCGACAACTAAGGTCGATGATAGTGCGGGACCATCGGGAAGC
* * *
3525 ATCGAACACCATCGAAAACTAAGGTC-GATGGTGGTGTAAGACCATCGGGAAGCATCGGTACCTT
1 ATCGAACACCATCGAAAACTAAGG-CAAATGGTGGTGTAAGACCATCGGGAAGCATCGGAACCAT
* * * * * *
3589 GGTACCTTGGATGTGCGAGAGCATCGGACACTATCGGTAACTTAGGTCGATGATGGTGCGGGACC
65 GGTACCTTCGATGTGAGAGAGCATCGAACACCATCGGTAACTGAGGCCGATGATGGTGCGGGACC
* * * * * * *
3654 ATCGGGATCCATCGGTACCTTGGTACCTTGGATGTGCGAGAGCATCGGACACCCTCGATAACTTA
130 ATCGAGAACCATCGGTACCATGGTACCTTCGATGTGCGAGAGCATCGAACACCATCGATAACATA
* * *
3719 GGCCGATGGTGGTGCCGGACCATCGGGAAGCATCGACACCTTGGTGCCTCGGATGTATG-GA-AG
195 GGCCGATGGTGATGCCGGACAATCGGGAACCATCGACACCTTGGTGCCTCGGATG--TGCGAGAG
* *
3782 CATCGGACACCATCGACAACTAAGG-CTGATGATAGTGCGGGACCATCGGGAAGT
258 CATCAGACACCATCGACAACTAAGGTC-GATGATAGTGCGGGACCATCGGGAAGC
3836 ATCG
1 ATCG
3840 GCACCATGGT
Statistics
Matches: 261, Mismatches: 50, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
310 1 0.00
311 255 0.98
312 3 0.01
313 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.21
Consensus pattern (311 bp):
ATCGAACACCATCGAAAACTAAGGCAAATGGTGGTGTAAGACCATCGGGAAGCATCGGAACCATG
GTACCTTCGATGTGAGAGAGCATCGAACACCATCGGTAACTGAGGCCGATGATGGTGCGGGACCA
TCGAGAACCATCGGTACCATGGTACCTTCGATGTGCGAGAGCATCGAACACCATCGATAACATAG
GCCGATGGTGATGCCGGACAATCGGGAACCATCGACACCTTGGTGCCTCGGATGTGCGAGAGCAT
CAGACACCATCGACAACTAAGGTCGATGATAGTGCGGGACCATCGGGAAGC
Found at i:3871 original size:397 final size:397
Alignment explanation
Indices: 3149--3925 Score: 922
Period size: 397 Copynumber: 2.0 Consensus size: 397
3139 TCGGTAGCTT
** * * * *
3149 AGGTCGATGGTGGTACGGGACCATCGAGAATCATCGGTACCTTGGTGCCTCAAATGTGCGGGAGT
1 AGGTCGATGGTGGTACAAGACCATCGAGAAGCATCGGTACCTTGGTACCTCAAATGTGCGAGAGC
* * **
3214 ATCGGACACCATCGGTAACTAAGGCAAATGGTGGTGTGGGACCATCGGGAAGTATCGGAACCATG
66 ATCGGACACCATCGGTAACTAAGGCAAATGATGGTGCGGGACCATCGGGAACCATCGGAACCATG
* * * * * *
3279 GTGCCTTCGATGTGAGGGTGCATCGAACACCATTGGTAACTGAGGCCGATGGTGGTGCGGGACCA
131 GTACCTTCGATGTGAGAGAGCATCGAACACCATCGATAACTGAGGCCGATGGTGGTGCCGGACCA
* ** **
3344 TCGAGAAGTATCGGTACCATGGTGCCTTCGATGTGCGATAGCATCGAACACCATCGGTAACATAG
196 TCGAGAAGCATCGACACCATGGTGCCTTCGATGTGCGATAGCATCGAACACCATCGACAACATAG
* * * * *
3409 GTCGATGGTGATGCGGGACAATCGGGATCCATCGGTACCTTGGTGCCTTGGATGTGCGAGAGCAT
261 GTCGATGATGATGCGGGACAATCGGGAACCATCGGCACCATGGTGCCTTCGATGTGCGAGAGCAT
* * * * *
3474 CAGACACCATCGGTAACTTAGGTCGATGGTGGTGCGGGTCTATCGGGAAGCATCGAACACCATCG
326 CAGACACCATCGGGAACTTAGGTCGATGGAGGTGCGGGACCATCGGAAAGCATCGAACACCATCG
3539 AAAACTA
391 AAAACTA
** * ***
3546 AGGTCGATGGTGGTGTAAGACCATCGGGAAGCATCGGTACCTTGGTACCTTGGATGTGCGAGAGC
1 AGGTCGATGGTGGTACAAGACCATCGAGAAGCATCGGTACCTTGGTACCTCAAATGTGCGAGAGC
* * * * * *
3611 ATCGGACACTATCGGTAACTTAGGTC-GATGATGGTGCGGGACCATCGGGATCCATCGGTACCTT
66 ATCGGACACCATCGGTAACTAAGG-CAAATGATGGTGCGGGACCATCGGGAACCATCGGAACCAT
* * * * *
3675 GGTACCTTGGATGTGCGAGAGCATCGGACACCCTCGATAACTTAGGCCGATGGTGGTGCCGGACC
130 GGTACCTTCGATGTGAGAGAGCATCGAACACCATCGATAACTGAGGCCGATGGTGGTGCCGGACC
* * *
3740 ATCGGGAAGCATCGACACCTTGGTGCC-TCGGATGTATG-GA-AGCATCGGACACCATCGACAAC
195 ATCGAGAAGCATCGACACCATGGTGCCTTC-GATG--TGCGATAGCATCGAACACCATCGACAAC
* **
3802 -TAAGG-CTGATGAT-AGTGCGGGACCATCGGGAAGTATCGGCACCATGGTGCCTTCGATGTGC-
257 AT-AGGTC-GATGATGA-TGCGGGACAATCGGGAACCATCGGCACCATGGTGCCTTCGATGTGCG
* *
3863 AGGAGCATCGGACATCATCGGGAACTTAGGTCGATGGAGGTGCGGGACCATCGGAAAGCATCG
319 A-GAGCATCAGACACCATCGGGAACTTAGGTCGATGGAGGTGCGGGACCATCGGAAAGCATCG
3926 GCACCTTGGT
Statistics
Matches: 316, Mismatches: 56, Indels: 16
0.81 0.14 0.04
Matches are distributed among these distances:
396 6 0.02
397 305 0.97
398 3 0.01
399 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (397 bp):
AGGTCGATGGTGGTACAAGACCATCGAGAAGCATCGGTACCTTGGTACCTCAAATGTGCGAGAGC
ATCGGACACCATCGGTAACTAAGGCAAATGATGGTGCGGGACCATCGGGAACCATCGGAACCATG
GTACCTTCGATGTGAGAGAGCATCGAACACCATCGATAACTGAGGCCGATGGTGGTGCCGGACCA
TCGAGAAGCATCGACACCATGGTGCCTTCGATGTGCGATAGCATCGAACACCATCGACAACATAG
GTCGATGATGATGCGGGACAATCGGGAACCATCGGCACCATGGTGCCTTCGATGTGCGAGAGCAT
CAGACACCATCGGGAACTTAGGTCGATGGAGGTGCGGGACCATCGGAAAGCATCGAACACCATCG
AAAACTA
Found at i:3949 original size:43 final size:43
Alignment explanation
Indices: 3816--3952 Score: 125
Period size: 43 Copynumber: 3.2 Consensus size: 43
3806 GCTGATGATA
* * *
3816 GTGCGGGACCATCGGGAAGTATCGGCACCATGGTGCCTT-CGAT
1 GTGCGGGACCATCGGAAAGCATCGGCACCTTGGTGCCTTGC-AT
* * * * * * ** * *
3859 GTGCAGGAGCATCGGACATCATCGGGAACTTAGGT-CGATGGAG
1 GTGCGGGACCATCGGAAAGCATCGGCACCTT-GGTGCCTTGCAT
3902 GTGCGGGACCATCGGAAAGCATCGGCACCTTGGTGCCTTGCAT
1 GTGCGGGACCATCGGAAAGCATCGGCACCTTGGTGCCTTGCAT
3945 GTGCGGGA
1 GTGCGGGA
3953 GCATGGGATA
Statistics
Matches: 68, Mismatches: 23, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
42 3 0.04
43 62 0.91
44 3 0.04
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.20
Consensus pattern (43 bp):
GTGCGGGACCATCGGAAAGCATCGGCACCTTGGTGCCTTGCAT
Done.