Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014433.1 Kokia drynarioides strain JFW-HI SEQ_129471, 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: 6152
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:5417 original size:59 final size:57
Alignment explanation
Indices: 5354--5518 Score: 167
Period size: 57 Copynumber: 2.8 Consensus size: 57
5344 TTGACACTCG
5354 GGGGTAAGATAATCA-ATTTTTAGAAGCTT-GGGGGAAAAATTG-TAATTTTTAGATAATTT
1 GGGGTAA-A-AATCATATTTTTAGAAG-TTCGGGGGAAAAA-TGATAA-TTTTAGATAATTT
* * *
5413 GGGGTTAAAAATTATATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTAGATAATTT
1 GGGG-TAAAAATCATATTTTTAGAAGTTCGGGGGAAAAATGATAATTTTAGATAATTT
* * * * *
5471 AGGGTTAAAAATGATA-TTTTGGAAGTTCGGGGGTAAAATGGTAATTTT
1 -GGGGTAAAAATCATATTTTTAGAAGTTCGGGGGAAAAATGATAATTTT
5519 GGAAGTTTAA
Statistics
Matches: 95, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
57 31 0.33
58 31 0.33
59 30 0.32
60 3 0.03
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (57 bp):
GGGGTAAAAATCATATTTTTAGAAGTTCGGGGGAAAAATGATAATTTTAGATAATTT
Found at i:5450 original size:29 final size:29
Alignment explanation
Indices: 5351--5990 Score: 111
Period size: 29 Copynumber: 21.9 Consensus size: 29
5341 TCTTTGACAC
* *
5351 TCGGGGGTAAGATAATCA-ATTTTTAGAAGCT
1 TCGGGGGTAA-A-AATTATATTTTTGGAAG-T
* * *
5382 T-GGGGG-AAAAATTGTAATTTTTAGATAAT
1 TCGGGGGTAAAAATTAT-ATTTTTGGA-AGT
* *
5411 TTGGGGTTAAAAATTATATTTTTGGAAGT
1 TCGGGGGTAAAAATTATATTTTTGGAAGT
* * * *
5440 TCGGGGGT-AAAATGATAATTTTAGATAAT
1 TCGGGGGTAAAAATTATATTTTTGGA-AGT
** * *
5469 TTAGGGTTAAAAATGATA-TTTTGGAAGT
1 TCGGGGGTAAAAATTATATTTTTGGAAGT
** *
5497 TCGGGGGT-AAAATGGTAATTTTGGAAGT
1 TCGGGGGTAAAAATTATATTTTTGGAAGT
*** *
5525 TTAAGGGTAAAAATGTGAT-TTTTTGGTAGT
1 TCGGGGGTAAAAAT-T-ATATTTTTGGAAGT
* * * *
5555 TCAGTGGT-AAAATGTATTTTTTTGAAAGT
1 TCGGGGGTAAAAAT-TATATTTTTGGAAGT
*** * **
5584 TTAAGGTTAAAAA-TGGATTTTTGGACA--
1 TCGGGGGTAAAAATTATATTTTTGGA-AGT
** *
5611 TCTAAGGGT-AAAATGGTA-ATTTTTTGAAAGT
1 TC-GGGGGTAAAAAT--TATA-TTTTTGGAAGT
* *
5642 TC-GGGGTCAAAAATGGA-ATTTTTGGAAAT
1 TCGGGGGT-AAAAAT-TATATTTTTGGAAGT
** * * *
5671 TAAGAGGT-AAAATGGTA-AATTTTGGAAAT
1 TCGGGGGTAAAAAT--TATATTTTTGGAAGT
* * * * *
5700 TCGAGTGTAAAATAGTA-ATTTTTGAAAACT
1 TCGGGGGTAAAA-ATTATATTTTTG-GAAGT
* * *
5730 TC--GCGTCAAGAATGATATTTTTGGAAGT
1 TCGGGGGT-AAAAATTATATTTTTGGAAGT
5758 TCGGGGGT-AAAATGGTA-ATTTTTGGAAGT
1 TCGGGGGTAAAAAT--TATATTTTTGGAAGT
* * *
5787 TTGGGGGAAAAAATGTGAT-TTTTTGGAAAT
1 TCGGGGGTAAAAAT-T-ATATTTTTGGAAGT
**
5817 TTAGGGGT-AAAATGTA-ATTTTTGGAAAGT
1 TCGGGGGTAAAAAT-TATATTTTTGG-AAGT
** * *
5846 TCAAGGGTAAAAA-TATAATTTGTGTGAAGC
1 TCGGGGGTAAAAATTAT-ATTTTTG-GAAGT
*
5876 TCGAGGGT-AAAATGTA-ATTTTTGTGAAGT
1 TCGGGGGTAAAAAT-TATATTTTTG-GAAGT
* * *
5905 TCGAGGGTCAAAATGTGAT-TTTTT-AAAGT
1 TCGGGGGTAAAAAT-T-ATATTTTTGGAAGT
* * *
5934 TTGGGAGT-CAAATTATAATTTTTGGAAAGT
1 TCGGGGGTAAAAATTAT-ATTTTTGG-AAGT
* * *
5964 TTGGGGG-ACAAATCATGATTTTTGGAA
1 TCGGGGGTAAAAATTAT-ATTTTTGGAA
5991 AAATTAGGGA
Statistics
Matches: 462, Mismatches: 94, Indels: 108
0.70 0.14 0.16
Matches are distributed among these distances:
26 2 0.00
27 17 0.04
28 90 0.19
29 180 0.39
30 146 0.32
31 27 0.06
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
TCGGGGGTAAAAATTATATTTTTGGAAGT
Found at i:5481 original size:58 final size:57
Alignment explanation
Indices: 5369--5597 Score: 218
Period size: 58 Copynumber: 3.9 Consensus size: 57
5359 AAGATAATCA
* * *
5369 ATTTTTAGAAGCTT-GGGGGAAAAATTGTAATTTTTAGATAATTTGGGGTTAAAAATTAT
1 ATTTTTGGAAG-TTCGGGGGTAAAA-TGTAA-TTTTAGATAATTTAGGGTTAAAAATTAT
*
5428 ATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTAGATAATTTAGGGTTAAAAATGAT
1 ATTTTTGGAAGTTCGGGGGTAAAATG-TAATTTTAGATAATTTAGGGTTAAAAATTAT
* *
5486 A-TTTTGGAAGTTCGGGGGTAAAATGGTAATTTTGGA-AGTTTAAGGG-TAAAAATGTGAT
1 ATTTTTGGAAGTTCGGGGGTAAAAT-GTAATTTTAGATAATTT-AGGGTTAAAAAT-T-AT
* * * * * *
5544 -TTTTTGGTAGTTCAGTGGTAAAATGTATTTTTTTGA-AAGTTTAAGGTTAAAAAT
1 ATTTTTGGAAGTTCGGGGGTAAAATGTA-ATTTTAGATAA-TTTAGGGTTAAAAAT
5598 GGATTTTTGG
Statistics
Matches: 146, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
56 11 0.08
57 39 0.27
58 64 0.44
59 32 0.22
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.40
Consensus pattern (57 bp):
ATTTTTGGAAGTTCGGGGGTAAAATGTAATTTTAGATAATTTAGGGTTAAAAATTAT
Found at i:5597 original size:30 final size:30
Alignment explanation
Indices: 5515--5642 Score: 99
Period size: 30 Copynumber: 4.4 Consensus size: 30
5505 AAAATGGTAA
5515 TTTTGGAAGTTTAAGGGTAAAAATGTGA-TT
1 TTTTGGAAGTTTAAGGGTAAAAATGT-ATTT
* *
5545 TTTTGGTAG-TTCAGTGGT-AAAATGTATTT
1 TTTTGGAAGTTTAAG-GGTAAAAATGTATTT
* * *
5574 TTTTGAAAGTTTAAGGTTAAAAATGGA--T
1 TTTTGGAAGTTTAAGGGTAAAAATGTATTT
* *
5602 TTTTGGACA-TCTAAGGGT-AAAATGGTAATT
1 TTTTGGA-AGTTTAAGGGTAAAAAT-GTATTT
*
5632 TTTTGAAAGTT
1 TTTTGGAAGTT
5643 CGGGGTCAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
27 5 0.07
28 17 0.22
29 24 0.32
30 30 0.39
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.42
Consensus pattern (30 bp):
TTTTGGAAGTTTAAGGGTAAAAATGTATTT
Found at i:5603 original size:58 final size:58
Alignment explanation
Indices: 5415--5684 Score: 207
Period size: 58 Copynumber: 4.7 Consensus size: 58
5405 GATAATTTGG
* * * * *
5415 GGTTAAAAAT-TATATTTTTGGAAGTTCGGGGGTAAAATG-ATAATTTTAGATAA-TTTAG
1 GGTTAAAAATGGAT-TTTTTGGAAGTTCAGGGGTAAAATGTAT-TTTTTTGA-AAGTTTAA
* * * *
5473 GGTTAAAAAT-GATATTTTGGAAGTTCGGGGGTAAAATGGTA--ATTTTGGAAGTTTAA
1 GGTTAAAAATGGATTTTTTGGAAGTTCAGGGGTAAAAT-GTATTTTTTTGAAAGTTTAA
* * *
5529 GGGTAAAAATGTGATTTTTTGGTAGTTCAGTGGTAAAATGTATTTTTTTGAAAGTTTAA
1 GGTTAAAAATG-GATTTTTTGGAAGTTCAGGGGTAAAATGTATTTTTTTGAAAGTTTAA
* * ***
5588 GGTTAAAAATGGA-TTTTTGGACA--TCTAAGGGTAAAATGGTAATTTTTTGAAAGTTCGG
1 GGTTAAAAATGGATTTTTTGGA-AGTTC-AGGGGTAAAAT-GTATTTTTTTGAAAGTTTAA
* * * * *
5646 GGTCAAAAATGGAATTTTTGGAAATTAAGAGGTAAAATG
1 GGTTAAAAATGGATTTTTTGGAAGTTCAGGGGTAAAATG
5685 GTAAATTTTG
Statistics
Matches: 174, Mismatches: 25, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
55 2 0.01
56 19 0.11
57 42 0.24
58 69 0.40
59 41 0.24
60 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (58 bp):
GGTTAAAAATGGATTTTTTGGAAGTTCAGGGGTAAAATGTATTTTTTTGAAAGTTTAA
Found at i:5662 original size:30 final size:28
Alignment explanation
Indices: 5616--5934 Score: 122
Period size: 29 Copynumber: 10.9 Consensus size: 28
5606 GGACATCTAA
5616 GGGTAAAATGGTAATTTTTTGAAAGTTCG
1 GGGTAAAATGG-AATTTTTTGAAAGTTCG
* *
5645 GGGTCAAAAATGGAATTTTTGGAAA-TTAAG
1 GGGT--AAAATGGAATTTTTTGAAAGTT-CG
* * *
5675 AGGTAAAATGGTAAATTTTGGAAA-TTCG
1 GGGTAAAATGG-AATTTTTTGAAAGTTCG
* * *
5703 AGTGTAAAATAGTAA-TTTTTGAAAACTTC-
1 -GGGTAAAAT-GGAATTTTTTG-AAAGTTCG
* *
5732 GCGTCAAGAAT-G-ATATTTTTGGAAGTTCGG
1 GGGT-AA-AATGGAAT-TTTTTGAAAGTTC-G
* *
5762 GGGTAAAATGGTAA-TTTTTGGAAGTTTGG
1 GGGTAAAATGG-AATTTTTTGAAAG-TTCG
* * *
5791 GGGAAAAAATGTG-ATTTTTTGGAAATTTAG
1 GGG-TAAAATG-GAATTTTTT-GAAAGTTCG
* * *
5821 GGGTAAAATGTAATTTTTGGAAAGTTCAA
1 GGGTAAAATGGAATTTTTTGAAAGTTC-G
** * *
5850 GGGTAAAAATATAATTTGTGTG-AAGCTCG
1 GGGT-AAAATGGAATTT-TTTGAAAGTTCG
*
5879 AGGGTAAAATGTAATTTTTGTG-AAGTTCG
1 -GGGTAAAATGGAATTTTT-TGAAAGTTCG
5908 AGGGTCAAAATGTG-ATTTTTT-AAAGTT
1 -GGGT-AAAATG-GAATTTTTTGAAAGTT
5935 TGGGAGTCAA
Statistics
Matches: 225, Mismatches: 34, Indels: 62
0.70 0.11 0.19
Matches are distributed among these distances:
27 1 0.00
28 31 0.14
29 103 0.46
30 76 0.34
31 14 0.06
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (28 bp):
GGGTAAAATGGAATTTTTTGAAAGTTCG
Found at i:5694 original size:58 final size:56
Alignment explanation
Indices: 5501--5711 Score: 169
Period size: 59 Copynumber: 3.6 Consensus size: 56
5491 GGAAGTTCGG
* * * * * *
5501 GGGTAAAATGGT-AATTTTGGAAGTTTAAGGGTAAAAATGTGATTTTTTGGTAGTTCA
1 GGGTAAAATGGTAAATTTTGAAAG-TTCAGGGTAAAAATG-GAATTTTTGGAAATTAA
** * * *
5558 GTGGTAAAAT-GTATTTTTTTGAAAGTTTAAGGTTAAAAATGG-ATTTTTGGACATCTAA
1 G-GGTAAAATGGTA-AATTTTGAAAG-TTCAGGGTAAAAATGGAATTTTTGGAAAT-TAA
* *
5616 GGGTAAAATGGTAATTTTTTGAAAGTTCGGGGTCAAAAATGGAATTTTTGGAAATTAA
1 GGGTAAAATGGTAA-ATTTTGAAAGTTCAGGGT-AAAAATGGAATTTTTGGAAATTAA
*
5674 GAGGTAAAATGGTAAATTTTGGAAA-TTCGAGTGTAAAA
1 G-GGTAAAATGGTAAATTTT-GAAAGTTC-AGGGTAAAA
5712 TAGTAATTTT
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
57 24 0.19
58 48 0.38
59 54 0.43
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (56 bp):
GGGTAAAATGGTAAATTTTGAAAGTTCAGGGTAAAAATGGAATTTTTGGAAATTAA
Found at i:5808 original size:87 final size:87
Alignment explanation
Indices: 5478--5927 Score: 279
Period size: 87 Copynumber: 5.2 Consensus size: 87
5468 TTTAGGGTTA
*
5478 AAAATGATA-TTTTGGAAGTTCGGGGGTAAAATGGTAA-TTTTGGAAGTTTAAGGGTAAAAAT-G
1 AAAATGATATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAGTTTAAGGG-AAAAATAG
* **
5540 TGATTTTTTGGTAGTTCAGTGGT-
65 TAATTTTTTGAAAGTTCAG-GGTC
* * * * * * *
5563 AAAATGTATTTTTTTGAAAGTTTAAGGTTAAAAATGG--ATTTTTGGACA-TCTAAGGGTAAAAT
1 AAAATG-ATATTTTTGGAAGTTCAGGGGT-AAAATGGTAATTTTTGGA-AGTTTAAGGGAAAAAT
* *
5625 GGTAATTTTTTGAAAGTTCGGGGTC
63 AGTAATTTTTTGAAAGTTCAGGGTC
* * * * * ** * *
5650 AAAAATGGA-ATTTTTGGAAATTAAGAGGTAAAATGGTAAATTTTGGAAATTCGAGTGTAAAATA
1 -AAAAT-GATATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAGTTTAAGGGAAAAATA
* *
5714 GTAA-TTTTTGAAAACTTC-GCGTC
64 GTAATTTTTTG-AAAGTTCAGGGTC
* **
5737 AAGAATGATATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTGGGGGAAAAA-AT
1 AA-AATGATATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAGTTTAAGGGAAAAATA-
* *
5801 GTGATTTTTTGGAAA-TTTAGGGGT-
64 GTAATTTTTT-GAAAGTTCA-GGGTC
* * * * ** *
5825 AAAATG-TAATTTTTGGAAAGTTCAAGGGTAAAAAT-ATAATTTGTGTGAAGCTCGAGGGTAAAA
1 AAAATGAT-ATTTTTGG-AAGTTCAGGGGT-AAAATGGTAATTTTTG-GAAGTTTAAGGGAAAAA
5888 T-GTAATTTTTGTG-AAGTTCGAGGGTC
62 TAGTAATTTTT-TGAAAGTTC-AGGGTC
5914 AAAATG-TGATTTTT
1 AAAATGAT-ATTTTT
5928 TAAAGTTTGG
Statistics
Matches: 285, Mismatches: 51, Indels: 54
0.73 0.13 0.14
Matches are distributed among these distances:
85 6 0.02
86 24 0.08
87 132 0.46
88 85 0.30
89 38 0.13
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (87 bp):
AAAATGATATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAGTTTAAGGGAAAAATAGT
AATTTTTTGAAAGTTCAGGGTC
Found at i:5828 original size:59 final size:58
Alignment explanation
Indices: 5742--5964 Score: 177
Period size: 59 Copynumber: 3.8 Consensus size: 58
5732 GCGTCAAGAA
* * * *
5742 TGATATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG-AAGTTTGGGGGAAAAAATG
1 TGAT-TTTTTGGAAATT-TGGGGTAAAAT-GTAATTTTTGGAAAGTTCGAGGGAAAAAATG
* * *
5802 TGATTTTTTGGAAATTTAGGGGTAAAATGTAATTTTTGGAAAGTTCAAGGGTAAAAATA
1 TGATTTTTTGGAAATTT-GGGGTAAAATGTAATTTTTGGAAAGTTCGAGGGAAAAAATG
* * ** * **
5861 T-AATTTGTGTGAAGCTCGAGGGTAAAATGTAATTTTTGTG-AAGTTCGAGGGTCAAAATG
1 TGATTTTTTG-GAAATTTG-GGGTAAAATGTAATTTTTG-GAAAGTTCGAGGGAAAAAATG
* *
5920 TGATTTTTT--AAAGTTTGGGAGTCAAATTATAATTTTTGGAAAGTT
1 TGATTTTTTGGAAA-TTTGGG-GT-AAAATGTAATTTTTGGAAAGTT
5965 TGGGGGACAA
Statistics
Matches: 131, Mismatches: 22, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
57 4 0.03
58 23 0.18
59 94 0.72
60 10 0.08
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (58 bp):
TGATTTTTTGGAAATTTGGGGTAAAATGTAATTTTTGGAAAGTTCGAGGGAAAAAATG
Found at i:5965 original size:30 final size:30
Alignment explanation
Indices: 5929--5991 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
5919 GTGATTTTTT
* *
5929 AAAGTTTGGGAGTCAAATTATAATTTTTGG
1 AAAGTTTGGGAGACAAATCATAATTTTTGG
* *
5959 AAAGTTTGGGGGACAAATCATGATTTTTGG
1 AAAGTTTGGGAGACAAATCATAATTTTTGG
5989 AAA
1 AAA
5992 AATTAGGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAGTTTGGGAGACAAATCATAATTTTTGG
Done.