Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009534.1 Kokia drynarioides strain JFW-HI SEQ_124246, 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: 26752
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:3568 original size:58 final size:58
Alignment explanation
Indices: 3506--3696 Score: 199
Period size: 58 Copynumber: 3.3 Consensus size: 58
3496 ATCGGGATAA
* *
3506 AAAATTAAATTTTTGAACATTCGGGGGCAAAATGGTAACTTTTTAGAGTTTCGAGGTC
1 AAAATTGAATTTTTGAACATTCGGGGGTAAAATGGTAACTTTTTAGAGTTTCGAGGTC
* * * * *
3564 AAAATGGAGTTTTT-AGACATTCGGGGGTAAAATGGTAACTTTTGAAAGTTTCGAGGTT
1 AAAATTGAATTTTTGA-ACATTCGGGGGTAAAATGGTAACTTTTTAGAGTTTCGAGGTC
* * ** * *
3622 AAAAATGAATTTTTGGAGGTTTGGGGGTAAAAT-GTAA-TTTTTGGAAGTTTCGAGGTC
1 AAAATTGAATTTTTGAACATTCGGGGGTAAAATGGTAACTTTTTAG-AGTTTCGAGGTC
* *
3679 AAAAATGGTATTTTTGAA
1 -AAAATTGAATTTTTGAA
3697 AGTTTCGAGG
Statistics
Matches: 107, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
56 4 0.04
57 16 0.15
58 87 0.81
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (58 bp):
AAAATTGAATTTTTGAACATTCGGGGGTAAAATGGTAACTTTTTAGAGTTTCGAGGTC
Found at i:3730 original size:60 final size:58
Alignment explanation
Indices: 3552--3754 Score: 214
Period size: 58 Copynumber: 3.5 Consensus size: 58
3542 AACTTTTTAG
* * * * * *
3552 AGTTTCGAGGTC-AAAATGGAGTTTTTAGACA-TTCGGGGGTAAAATGGTAACTTTTGAA
1 AGTTTCGAGGTCAAAAATGGAATTTTT-GAAAGTTTGAGGGTAAAAT-GAAATTTTTGAA
* * * * * *
3610 AGTTTCGAGGTTAAAAAT-GAATTTTTGGAGGTTTGGGGGTAAAATGTAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGAAAGTTTGAGGGTAAAATGAAATTTTTGAA
* *
3667 AGTTTCGAGGTCAAAAATGGTATTTTTGAAAGTTTCGAGGTTAAAAATGAAATTTTTGAA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGAAAGTTT-GAGGGT-AAAATGAAATTTTTGAA
*
3727 AGTTTTGAGGTCAAAAATGGAATTTTTG
1 AGTTTCGAGGTCAAAAATGGAATTTTTG
3755 GATAGTTTAG
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
57 28 0.23
58 44 0.36
59 9 0.07
60 41 0.34
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (58 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGAAAGTTTGAGGGTAAAATGAAATTTTTGAA
Found at i:3754 original size:30 final size:30
Alignment explanation
Indices: 3534--3754 Score: 190
Period size: 30 Copynumber: 7.5 Consensus size: 30
3524 ATTCGGGGGC
*
3534 AAAATGGTAACTTTTT-AGAGTTTCGAGGTC-
1 AAAATGG-AA-TTTTTGAAAGTTTCGAGGTCA
* * *
3564 AAAATGGAGTTTTTAGACA--TTCGGGGGT--
1 AAAATGGAATTTTT-GAAAGTTTC-GAGGTCA
* *
3592 AAAATGGTAACTTTTGAAAGTTTCGAGGTTA
1 AAAATGG-AATTTTTGAAAGTTTCGAGGTCA
* * * *
3623 AAAAT-GAATTTTTGGAGGTTTGGGGGT--
1 AAAATGGAATTTTTGAAAGTTTCGAGGTCA
* *
3650 AAAATGTAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGAAAGTTTCGAGGTCA
* *
3680 AAAATGGTATTTTTGAAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGAAAGTTTCGAGGTCA
* *
3710 AAAATGAAATTTTTGAAAGTTTTGAGGTCA
1 AAAATGGAATTTTTGAAAGTTTCGAGGTCA
3740 AAAATGGAATTTTTG
1 AAAATGGAATTTTTG
3755 GATAGTTTAG
Statistics
Matches: 155, Mismatches: 25, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
27 5 0.03
28 36 0.23
29 30 0.19
30 79 0.51
31 5 0.03
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTGAAAGTTTCGAGGTCA
Found at i:4882 original size:28 final size:25
Alignment explanation
Indices: 4844--4903 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 25
4834 TTTTTTTATT
*
4844 TAATTATTATTAATGTTGTAATTAATAA
1 TAATTAATATT-ATGTT-TAA-TAATAA
*
4872 TAATTAATATTATGTTTAATATTAA
1 TAATTAATATTATGTTTAATAATAA
4897 T-ATTAAT
1 TAATTAAT
4904 GATAATTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.20
25 6 0.20
26 3 0.10
27 5 0.17
28 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (25 bp):
TAATTAATATTATGTTTAATAATAA
Found at i:5858 original size:29 final size:30
Alignment explanation
Indices: 5826--6174 Score: 291
Period size: 30 Copynumber: 12.0 Consensus size: 30
5816 TGGACCTCTG
*
5826 GGGGT-AAAAGGGTAATTTTTGGAAGTTTC
1 GGGGTCAAAATGGTAATTTTTGGAAGTTTC
*
5855 GGGGTCAAAATGG-AA-TTTTGGAAGTTTA
1 GGGGTCAAAATGGTAATTTTTGGAAGTTTC
* *
5883 GGGGT--AAATAGTAATTTTT-GAGAGTTTT
1 GGGGTCAAAATGGTAATTTTTGGA-AGTTTC
* *
5911 GAGGTCAAAAATGG-AATTTTTGG-AGGTTC
1 GGGGTC-AAAATGGTAATTTTTGGAAGTTTC
*
5940 AGGGGT-AAAATGGTAATTTTTGAAAGTTTC
1 -GGGGTCAAAATGGTAATTTTTGGAAGTTTC
* * *
5970 TGGGTCAAAATCG-AGATTTTTGAAAG-TTC
1 GGGGTCAAAATGGTA-ATTTTTGGAAGTTTC
*
5999 GGGGT-AAAATGGTAATTTTGGGAAGTTTC
1 GGGGTCAAAATGGTAATTTTTGGAAGTTTC
** * *
6028 AAGGTCAAAATTGG-GATTTTTGGAAGTTTG
1 GGGGTCAAAA-TGGTAATTTTTGGAAGTTTC
*
6058 GGGGTAAAAAT-GTAATTTTTGGAAGTTTC
1 GGGGTCAAAATGGTAATTTTTGGAAGTTTC
** ** *
6087 ACGGTCAAAAT-CAAGATTTTTGGAAGTTTA
1 GGGGTCAAAATGGTA-ATTTTTGGAAGTTTC
* * *
6117 GGGGTAAAAAT-GTAATTTTTGAAAGTTTT
1 GGGGTCAAAATGGTAATTTTTGGAAGTTTC
*
6146 GGGGTCAAAATCG-AGATTTTTGGAAGTTT
1 GGGGTCAAAATGGTA-ATTTTTGGAAGTTT
6175 AAGGACCTTT
Statistics
Matches: 257, Mismatches: 42, Indels: 41
0.76 0.12 0.12
Matches are distributed among these distances:
26 5 0.02
27 4 0.02
28 53 0.21
29 86 0.33
30 100 0.39
31 9 0.04
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.36
Consensus pattern (30 bp):
GGGGTCAAAATGGTAATTTTTGGAAGTTTC
Found at i:5968 original size:59 final size:59
Alignment explanation
Indices: 5826--6175 Score: 385
Period size: 59 Copynumber: 6.0 Consensus size: 59
5816 TGGACCTCTG
* * * * *
5826 GGGGTAAAAGGGTAATTTTTGGAAGTTTCGGGGTCAAAAT-G-GAATTTTGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAATCGAGATTTTTGGAAGTTTA
* * * * *
5883 GGGGT-AAATAGTAATTTTTGAGAGTTTTGAGGTCAAAAATGGA-ATTTTTGGAGGTTCA
1 GGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTC-AAAATCGAGATTTTTGGAAGTTTA
* *
5941 GGGGTAAAATGGTAATTTTTGAAAGTTTCTG-GGTCAAAATCGAGATTTTTGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGAAAGTTT-TGAGGTCAAAATCGAGATTTTTGGAAGTTTA
* * ** * * *
5999 GGGGTAAAATGGTAATTTTGGGAAGTTTCAAGGTCAAAATTGGGATTTTTGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAATCGAGATTTTTGGAAGTTTA
* * *
6058 GGGGTAAAAAT-GTAATTTTTGGAAG-TTTCACGGTCAAAATCAAGATTTTTGGAAGTTTA
1 GGGGT-AAAATGGTAATTTTTGAAAGTTTTGA-GGTCAAAATCGAGATTTTTGGAAGTTTA
*
6117 GGGGTAAAAAT-GTAATTTTTGAAAGTTTTGGGGTCAAAATCGAGATTTTTGGAAGTTTA
1 GGGGT-AAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAATCGAGATTTTTGGAAGTTTA
6176 AGGACCTTTA
Statistics
Matches: 247, Mismatches: 35, Indels: 20
0.82 0.12 0.07
Matches are distributed among these distances:
56 23 0.09
57 10 0.04
58 76 0.31
59 128 0.52
60 10 0.04
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.36
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAATCGAGATTTTTGGAAGTTTA
Found at i:7909 original size:17 final size:17
Alignment explanation
Indices: 7884--7938 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
7874 TAACTGGACT
*
7884 TTTTTAATTAATTTAAA
1 TTTTAAATTAATTTAAA
* *
7901 TTTTAAATTCAAATTGAA
1 TTTTAAATT-AATTTAAA
7919 -TTTAAACTTAATTTAAA
1 TTTTAAA-TTAATTTAAA
7936 TTT
1 TTT
7939 AAACTTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 20 0.67
18 10 0.33
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTTAAATTAATTTAAA
Found at i:7939 original size:17 final size:17
Alignment explanation
Indices: 7891--7978 Score: 79
Period size: 17 Copynumber: 5.0 Consensus size: 17
7881 ACTTTTTTAA
*
7891 TTAATTTAAATTTTAAA-
1 TTAAATTAAA-TTTAAAC
*
7908 TTCAAATTGAATTTAAAC
1 TT-AAATTAAATTTAAAC
*
7926 TTAATTTAAATTTAAAC
1 TTAAATTAAATTTAAAC
**
7943 TTAAAAGAAAAGTTTAAAC
1 TT-AAATTAAA-TTTAAAC
*
7962 TTAAACTAAATTTAAAC
1 TTAAATTAAATTTAAAC
7979 CCAAAATGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
17 30 0.52
18 19 0.33
19 9 0.16
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (17 bp):
TTAAATTAAATTTAAAC
Found at i:8808 original size:17 final size:17
Alignment explanation
Indices: 8780--8859 Score: 108
Period size: 17 Copynumber: 4.7 Consensus size: 17
8770 ATTTTAAAGT
* *
8780 TTTAAGTTTAAAAT-TA
1 TTTAAATTTAAAATGAA
* *
8796 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATGAA
8814 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATGAA
8831 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATGAA
8848 TTTAAATTTAAA
1 TTTAAATTTAAA
8860 TTTAAAGTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
16 3 0.05
17 50 0.88
18 4 0.07
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATGAA
Found at i:8816 original size:11 final size:11
Alignment explanation
Indices: 8800--8878 Score: 77
Period size: 11 Copynumber: 7.0 Consensus size: 11
8790 AAATTATTTC
*
8800 AAATTTAAACT
1 AAATTTAAATT
8811 AAATTTAAATTT
1 AAATTTAAA-TT
* * *
8823 AAAATGAATTT
1 AAATTTAAATT
*
8834 AAATTTAAAAT
1 AAATTTAAATT
*
8845 GAATTTAAATTT
1 AAATTTAAA-TT
*
8857 AAATTTAAAGT
1 AAATTTAAATT
8868 AAATTTAAATT
1 AAATTTAAATT
8879 TAGAAATAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
11 37 0.70
12 16 0.30
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:8840 original size:23 final size:23
Alignment explanation
Indices: 8829--8880 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
8819 ATTTAAAATG
*
8829 AATTTAAATTTAAAATGAATTTA
1 AATTTAAATTTAAAATAAATTTA
*
8852 AATTTAAATTTAAAGTAAATTTA
1 AATTTAAATTTAAAATAAATTTA
8875 AATTTA
1 AATTTA
8881 GAAATAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
AATTTAAATTTAAAATAAATTTA
Found at i:8844 original size:7 final size:6
Alignment explanation
Indices: 8795--8880 Score: 81
Period size: 6 Copynumber: 14.8 Consensus size: 6
8785 GTTTAAAATT
* * *
8795 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ATGA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
8842 A-ATGA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA
8881 GAAATAAATC
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
5 14 0.22
6 45 0.71
7 4 0.06
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:10676 original size:24 final size:23
Alignment explanation
Indices: 10649--10697 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
10639 ATATAAAAAT
10649 ATGTAATAAAAAAA-TTATATTTTG
1 ATGT-ATAAAAAAATTTA-ATTTTG
* *
10673 ATGTTTAAAATAATTTAATTTTG
1 ATGTATAAAAAAATTTAATTTTG
10696 AT
1 AT
10698 TCTCTTAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (23 bp):
ATGTATAAAAAAATTTAATTTTG
Found at i:11319 original size:17 final size:16
Alignment explanation
Indices: 11284--11313 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11274 ATTACATATG
11284 AATTTTATATAAATTT
1 AATTTTATATAAATTT
11300 AATTTT-TATAAATT
1 AATTTTATATAAATT
11314 ATTAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTATATAAATTT
Found at i:12005 original size:15 final size:16
Alignment explanation
Indices: 11984--12024 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
11974 TAATCCTTTA
11984 AAAATTATAAAGATA-T
1 AAAATTATAAA-ATATT
12000 -AAATTATTAAAATATT
1 AAAATTA-TAAAATATT
12016 AAAATTATA
1 AAAATTATA
12025 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AAAATTATAAAATATT
Found at i:13399 original size:63 final size:63
Alignment explanation
Indices: 13300--13435 Score: 245
Period size: 63 Copynumber: 2.2 Consensus size: 63
13290 ATGTATGTCT
*
13300 AATAAAATAAAATCTTGAAAATCAACTATGGTGGAATAATTTGGCATTAGTCAAGGTCTCTCC
1 AATAAAATAAAATCTTGAAAATCAACTATAGTGGAATAATTTGGCATTAGTCAAGGTCTCTCC
*
13363 AATAAAATAAAATCTTGAAAATCAACTATAGTGGAATAATTTGGCATTAGTCAAGGTGTCTCC
1 AATAAAATAAAATCTTGAAAATCAACTATAGTGGAATAATTTGGCATTAGTCAAGGTCTCTCC
*
13426 GATAAAATAA
1 AATAAAATAA
13436 TTTTTTTTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (63 bp):
AATAAAATAAAATCTTGAAAATCAACTATAGTGGAATAATTTGGCATTAGTCAAGGTCTCTCC
Found at i:23301 original size:19 final size:20
Alignment explanation
Indices: 23271--23309 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
23261 CCATTTTAAG
*
23271 TTTATAATATTATGTTATTT
1 TTTATAATATTATGTGATTT
23291 TTTAT-ATATTATGTGATTT
1 TTTATAATATTATGTGATTT
23310 AAAACACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTATAATATTATGTGATTT
Found at i:23748 original size:28 final size:29
Alignment explanation
Indices: 23716--23773 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
23706 TAATAATGGT
*
23716 ATTAATGATTTATAAA-A-ACATAAATTAA
1 ATTAATGATATATAAATATACA-AAATTAA
*
23744 ATTAATTATATATAAATATACAAAATTAA
1 ATTAATGATATATAAATATACAAAATTAA
23773 A
1 A
23774 ATAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 14 0.54
29 9 0.35
30 3 0.12
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (29 bp):
ATTAATGATATATAAATATACAAAATTAA
Done.