Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009551.1 Kokia drynarioides strain JFW-HI SEQ_124263, 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: 45254
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:873 original size:19 final size:19
Alignment explanation
Indices: 846--885 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
836 GAAATAATTA
846 TTAAAAATTTTATTT-ATTT
1 TTAAAAATTTT-TTTGATTT
*
865 TTAAGAATTTTTTTGATTT
1 TTAAAAATTTTTTTGATTT
884 TT
1 TT
886 TAAATGTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
TTAAAAATTTTTTTGATTT
Found at i:6208 original size:30 final size:30
Alignment explanation
Indices: 6166--6502 Score: 210
Period size: 30 Copynumber: 11.4 Consensus size: 30
6156 AAAGGTCTCT
*
6166 AAAC-TTCACAAAAATCACATTTTGACCCTC
1 AAACTTTC-CAAAAATTACATTTTGACCCTC
* *
6196 AAACTTTCCAAAAATTATAATTTGACCACT-
1 AAACTTTCCAAAAATTACATTTTGACC-CTC
* *
6226 AAACATTT-CAAAAATTAGATTTTAACCCTC
1 AAAC-TTTCCAAAAATTACATTTTGACCCTC
* *
6256 AAACTTTCTAAGAATTACATTTTGACCC-C
1 AAACTTTCCAAAAATTACATTTTGACCCTC
* * *
6285 TAAACGTACC-AAAATTACATTTTAACCC-C
1 -AAACTTTCCAAAAATTACATTTTGACCCTC
* * *
6314 TAAAC-TTCATAAAAATTATATTTTGACCCTT
1 -AAACTTTC-CAAAAATTACATTTTGACCCTC
* * *
6345 ATAC-TTCACAAAAATTATATTTTAACCCT-
1 AAACTTTC-CAAAAATTACATTTTGACCCTC
* *
6374 AAATTTTTCC-AAAATTGCATTTTTGACTCCT-
1 AAA-CTTTCCAAAAATTACA-TTTTGAC-CCTC
*
6405 AAA-TTTCCCAAAATTACATTTTGA-CC-C
1 AAACTTTCCAAAAATTACATTTTGACCCTC
6432 AAACTCATT-C-AAAATTACCATTTT-ACCCTC
1 AAACT--TTCCAAAAATTA-CATTTTGACCCTC
* * *
6462 GAAC-ATCC-AAAATTACCATTTTGCCCCTC
1 AAACTTTCCAAAAATTA-CATTTTGACCCTC
6491 AAA-TTTCCAAAA
1 AAACTTTCCAAAA
6503 GTTCGATTCT
Statistics
Matches: 248, Mismatches: 34, Indels: 50
0.75 0.10 0.15
Matches are distributed among these distances:
27 6 0.02
28 26 0.10
29 67 0.27
30 132 0.53
31 17 0.07
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.34
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTGACCCTC
Found at i:6499 original size:29 final size:29
Alignment explanation
Indices: 6379--6502 Score: 82
Period size: 29 Copynumber: 4.3 Consensus size: 29
6369 ACCCTAAATT
* *
6379 TTTCCAAAATT-GCATTTTTGACTCCT-AAA
1 TTTCCAAAATTACCA-TTTTG-CCCCTCAAA
*
6408 TTTCCCAAAATTA-CATTTTG-ACC-CAAA
1 TTT-CCAAAATTACCATTTTGCCCCTCAAA
* *
6435 CTCATT-CAAAATTACCATTTT-ACCCTCGAA
1 -T--TTCCAAAATTACCATTTTGCCCCTCAAA
**
6465 CATCCAAAATTACCATTTTGCCCCTCAAA
1 TTTCCAAAATTACCATTTTGCCCCTCAAA
6494 TTTCCAAAA
1 TTTCCAAAA
6503 GTTCGATTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
27 6 0.08
28 24 0.32
29 30 0.40
30 15 0.20
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTCCAAAATTACCATTTTGCCCCTCAAA
Found at i:9455 original size:17 final size:17
Alignment explanation
Indices: 9420--9455 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9410 AATAGTAAAA
**
9420 TTTTAATTTATAATTTT
1 TTTTAATTTATAAAATT
9437 TTTTAATTTATAAAATT
1 TTTTAATTTATAAAATT
9454 TT
1 TT
9456 AAGTCAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATTTATAAAATT
Found at i:12421 original size:39 final size:39
Alignment explanation
Indices: 12362--12447 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 39
12352 CTGCTTAAAT
*
12362 CAAATGGACAGGTGCTATACTATCCATCTCAAGCATAAC
1 CAAATGGACAGGTGCCATACTATCCATCTCAAGCATAAC
12401 CAAATGGACAGGTGCCATACTATCCATCTCAAGCATAAC
1 CAAATGGACAGGTGCCATACTATCCATCTCAAGCATAAC
*
12440 CAATTGGA
1 CAAATGGA
12448 GGCTTAGACT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (39 bp):
CAAATGGACAGGTGCCATACTATCCATCTCAAGCATAAC
Found at i:16832 original size:10 final size:10
Alignment explanation
Indices: 16817--16873 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 10
16807 TGATATATGA
16817 AAAAAATTAT
1 AAAAAATTAT
16827 AAAAAA-TA-
1 AAAAAATTAT
16835 AAAATAA--AT
1 AAAA-AATTAT
16844 AAAAAAGTTAT
1 AAAAAA-TTAT
16855 AAAAAATTAAT
1 AAAAAATT-AT
*
16866 TAAAAATT
1 AAAAAATT
16874 CTTTTTTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
8 7 0.17
9 8 0.20
10 8 0.20
11 17 0.43
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:17183 original size:16 final size:16
Alignment explanation
Indices: 17162--17196 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
17152 TATTCTCCAC
17162 CATTTAAAATCAGAAA
1 CATTTAAAATCAGAAA
*
17178 CATTTAAAATTAGAAA
1 CATTTAAAATCAGAAA
17194 CAT
1 CAT
17197 CTTATCCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (16 bp):
CATTTAAAATCAGAAA
Found at i:19730 original size:43 final size:43
Alignment explanation
Indices: 19662--19883 Score: 245
Period size: 43 Copynumber: 5.3 Consensus size: 43
19652 AGCGCCGCAA
***
19662 AAACGCCGCTATAGAACACAATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGTTCTTTAGCGGCGCTTTTCCCAC
* ** * *
19705 AAACGCCGCTATAGAACATGTTCTTTAGTGATGCTTTTTCCAT
1 AAACGCCGCTATAGAACATGTTCTTTAGCGGCGCTTTTCCCAC
19748 AAACGCCGCTATAGAACATGTTCTTTAGCGGCGCTTTT-CC-C
1 AAACGCCGCTATAGAACATGTTCTTTAGCGGCGCTTTTCCCAC
** **
19789 --ACGCCGCTATAGAATGTGTTCTTTAATGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGTTCTTTAGCGGCGCTTTTCCCAC
** * * * *
19830 AAACGCCTTTATAGAACATATTCTTTAGCTGTGCTTTTACCAC
1 AAACGCCGCTATAGAACATGTTCTTTAGCGGCGCTTTTCCCAC
*
19873 AAACACCGCTA
1 AAACGCCGCTA
19884 ATATTAACAA
Statistics
Matches: 146, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
39 32 0.22
40 2 0.01
41 1 0.01
42 2 0.01
43 109 0.75
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGTTCTTTAGCGGCGCTTTTCCCAC
Found at i:19843 original size:82 final size:82
Alignment explanation
Indices: 19662--19872 Score: 251
Period size: 82 Copynumber: 2.5 Consensus size: 82
19652 AGCGCCGCAA
* *
19662 AAACGCCGCTATAGAACACAATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGTT
1 AAACGCCGCTATAGAACATATTCTTTAGCGGCGCTTTT-CC-C--ACGCCGCTATAGAACATGTT
* * * *
19727 CTTTAGTGATGCTTTTTCCAT
62 CTTTAATGACGCTTTTCCCAC
* **
19748 AAACGCCGCTATAGAACATGTTCTTTAGCGGCGCTTTTCCCACGCCGCTATAGAATGTGTTCTTT
1 AAACGCCGCTATAGAACATATTCTTTAGCGGCGCTTTTCCCACGCCGCTATAGAACATGTTCTTT
*
19813 AATGGCGCTTTTCCCAC
66 AATGACGCTTTTCCCAC
** * * *
19830 AAACGCCTTTATAGAACATATTCTTTAGCTGTGCTTTTACCAC
1 AAACGCCGCTATAGAACATATTCTTTAGCGGCGCTTTTCCCAC
19873 AAACACCGCT
Statistics
Matches: 109, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
82 71 0.65
84 1 0.01
85 2 0.02
86 35 0.32
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.32
Consensus pattern (82 bp):
AAACGCCGCTATAGAACATATTCTTTAGCGGCGCTTTTCCCACGCCGCTATAGAACATGTTCTTT
AATGACGCTTTTCCCAC
Found at i:23698 original size:6 final size:6
Alignment explanation
Indices: 23687--23716 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
23677 GAAATATCGC
*
23687 AAAGAA AAAGAA AAAGAA AAAGAA ACAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
23717 CACATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:25898 original size:24 final size:22
Alignment explanation
Indices: 25866--25910 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
25856 CTTCGTGAAA
*
25866 ATCTATTTTCATATTTGTTTTTTT
1 ATCTATTTT--TATTCGTTTTTTT
*
25890 ATCTCTTTTTATTCGTTTTTT
1 ATCTATTTTTATTCGTTTTTT
25911 ATTTTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.71
Consensus pattern (22 bp):
ATCTATTTTTATTCGTTTTTTT
Found at i:27043 original size:49 final size:49
Alignment explanation
Indices: 26990--27563 Score: 400
Period size: 49 Copynumber: 11.7 Consensus size: 49
26980 GGCTTTTGGC
* * *
26990 TATAAGATTCGCCGTTGCGGCATAAATCTTTCCCTTCATGTTTTTGAGG
1 TATAGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGAGG
* * * * * * *
27039 TATAAGG-TTCACCGTTACGACTTAAACCTTTCCCTCCAT-ATCTTCACGG
1 TAT-AGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGA-GG
* * * *
27088 TACT-GGATTCACCGTTACGGCTTAAATCTTTCCCTTCATGTTTTTTAGG
1 TA-TAGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGAGG
* * * * * * *
27137 TGTAAGG-TTCGCCATTGTGACTTAAACCTTTCCCTTCAT-ATCTTCATGG
1 TAT-AGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGA-GG
* ** * *
27186 TACT-GGATTCGTCGTTATGGCTTAAATCTTTCCCTTCATGTTTTTGATG
1 TA-TAGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGAGG
* ** * * * *
27235 TACAAGG-TTCGCCGTTGTTACTTAAA-CTTTTCCCTTCATATCTTCGTGG
1 TA-TAGGATTCGCCGTTGCGACTTAAATC-TTTCCCTTCATGTTTTTGAGG
* * * * * *
27284 TTTTGGATTCGCTGTTGCGGCTTAAATCCTTCCCTTCATGTTCTTGAGG
1 TATAGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGAGG
* * * * * * *
27333 TACAGGGTTCGCCGTTGCGACTTAAACCTTT-CCTTCCATATCTTCGTGG
1 TATAGGATTCGCCGTTGCGACTTAAATCTTTCCCTT-CATGTTTTTGAGG
* *
27382 TACT-GGATTCGCCGTTACGACTTAAATGTTTCCCTTCATGTTTTTGAGG
1 TA-TAGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGAGG
* * * * * * * *
27431 TACAGGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGG
1 TATAGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGAGG
* * *
27480 TACT-GGATTTGCCGTTACGACTTAAATCTTTCCCTTCATGTTTCTGAGG
1 TA-TAGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGAGG
*
27529 TATAAGG-TTCGCCGTTACGACTTAAA-CGTTTCCCT
1 TAT-AGGATTCGCCGTTGCGACTTAAATC-TTTCCCT
27564 CTAAACCTGT
Statistics
Matches: 399, Mismatches: 103, Indels: 46
0.73 0.19 0.08
Matches are distributed among these distances:
48 22 0.06
49 354 0.89
50 23 0.06
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (49 bp):
TATAGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTTGAGG
Found at i:27122 original size:98 final size:98
Alignment explanation
Indices: 26995--27564 Score: 789
Period size: 98 Copynumber: 5.8 Consensus size: 98
26985 TTGGCTATAA
* * * * *
26995 GATTCGCCGTTGCGGCATAAATCTTTCCCTTCATGTTTTTGAGGTATAAGGTTCACCGTTACGAC
1 GATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGAC
**
27060 TTAAACCTTTCCCTCCATATCTTCACGGTACTG
66 TTAAACCTTTCCCTCCATATCTTCGTGGTACTG
* * ** * *
27093 GATTCACCGTTACGGCTTAAATCTTTCCCTTCATGTTTTTTAGGTGTAAGGTTCGCCATTGTGAC
1 GATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGAC
* *
27158 TTAAACCTTTCCCTTCATATCTTCATGGTACTG
66 TTAAACCTTTCCCTCCATATCTTCGTGGTACTG
* * * **
27191 GATTCGTCGTTATGGCTTAAATCTTTCCCTTCATGTTTTTGATGTACAAGGTTCGCCGTTGTTAC
1 GATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGAC
* * **
27256 TTAAACTTTTCCCTTCATATCTTCGTGGTTTTG
66 TTAAACCTTTCCCTCCATATCTTCGTGGTACTG
* * * * *
27289 GATTCGCTGTTGCGGCTTAAATCCTTCCCTTCATGTTCTTGAGGTACAGGGTTCGCCGTTGCGAC
1 GATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGAC
*
27354 TTAAACCTTTCCTTCCATATCTTCGTGGTACTG
66 TTAAACCTTTCCCTCCATATCTTCGTGGTACTG
* * *
27387 GATTCGCCGTTACGACTTAAATGTTTCCCTTCATGTTTTTGAGGTACAGGGTTCGCCGTTGCGAC
1 GATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGAC
27452 TTAAACCTTTCCCTCCATATCTTCGTGGTACTG
66 TTAAACCTTTCCCTCCATATCTTCGTGGTACTG
* * * * *
27485 GATTTGCCGTTACGACTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCGCCGTTACGAC
1 GATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGAC
*
27550 TTAAACGTTTCCCTC
66 TTAAACCTTTCCCTC
27565 TAAACCTGTA
Statistics
Matches: 419, Mismatches: 53, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 419 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (98 bp):
GATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCGCCGTTGCGAC
TTAAACCTTTCCCTCCATATCTTCGTGGTACTG
Found at i:44365 original size:30 final size:30
Alignment explanation
Indices: 44275--44476 Score: 216
Period size: 30 Copynumber: 7.1 Consensus size: 30
44265 GGATACCCGG
*
44275 GGGT-AAAATGGTAATTTTTGAAAGTTTCG-
1 GGGTAAAAATGG-AATTTTTGGAAGTTTCGA
* * *
44304 GGATCAAAAATGGAAATTTTGGATG-TTCGA
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCGA
44334 GGGTAAAAATGGAATTTTTGGAAGTTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGA
44364 GGGTAAAAATGGAATTTTTGGAAGTTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGA
* *
44394 GGTTAAAAATGGAATTTTTGG--G-GTC--
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGA
44419 ----AAAAATGGAATTTTTGGAAG-TTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGA
* *
44444 GGGTAAAAATGAAATTTTTGGGAGTTTCG-
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGA
44473 GGGT
1 GGGT
44477 CTTCGGGATA
Statistics
Matches: 148, Mismatches: 12, Indels: 26
0.80 0.06 0.14
Matches are distributed among these distances:
21 17 0.11
23 3 0.02
27 2 0.01
28 1 0.01
29 47 0.32
30 71 0.48
31 7 0.05
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.34
Consensus pattern (30 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCGA
Found at i:44462 original size:50 final size:50
Alignment explanation
Indices: 44364--44465 Score: 170
Period size: 50 Copynumber: 2.0 Consensus size: 50
44354 GAAGTTTCGA
* *
44364 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGAAATTTTTG
44414 GGGTCAAAAATGGAATTTTTGGAAG-TTCGAGGGTAAAAATGAAATTTTTG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGAAATTTTTG
44464 GG
1 GG
44466 AGTTTCGGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 29 0.59
51 20 0.41
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (50 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTAAAAATGAAATTTTTG
Found at i:44476 original size:29 final size:29
Alignment explanation
Indices: 44413--44477 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
44403 TGGAATTTTT
*
44413 GGGGTCAAAAATGGAATTTTTGGAAGTTC
1 GGGGTCAAAAATGAAATTTTTGGAAGTTC
*
44442 GAGGGT-AAAAATGAAATTTTTGGGAGTTTC
1 G-GGGTCAAAAATGAAATTTTTGGAAG-TTC
44472 GGGGTC
1 GGGGTC
44478 TTCGGGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.29, C:0.06, G:0.34, T:0.31
Consensus pattern (29 bp):
GGGGTCAAAAATGAAATTTTTGGAAGTTC
Done.