Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013573.1 Kokia drynarioides strain JFW-HI SEQ_128599, 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: 8102
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2993 original size:57 final size:56
Alignment explanation
Indices: 2905--3017 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 56
2895 GTATTTCTCC
*
2905 TCTATTTGTTTGGGGAGATCTTCTCTTATTATTTCGTCAAAATTTGGGATACCCAA
1 TCTATTTGTTTGGGGAGATCTTCTCTTATTATTTCGTCAAAATCTGGGATACCCAA
2961 NTCTATTTGTTTGGGGAGATCTTCTCTTATTATTTCGTCAAAATCTGGGATACCCAA
1 -TCTATTTGTTTGGGGAGATCTTCTCTTATTATTTCGTCAAAATCTGGGATACCCAA
3018 ATTCGCGACA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (56 bp):
TCTATTTGTTTGGGGAGATCTTCTCTTATTATTTCGTCAAAATCTGGGATACCCAA
Found at i:6962 original size:96 final size:96
Alignment explanation
Indices: 6778--6969 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
6768 TTTTTACGGA
** *
6778 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
6843 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * * **
6874 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTTCACCTAGTGAGTTAAGGCACAA-ATTTTT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
6938 GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
66 G-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
6970 TTAAAGCTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
95 6 0.07
96 72 0.87
97 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:7420 original size:30 final size:29
Alignment explanation
Indices: 7322--7704 Score: 306
Period size: 30 Copynumber: 13.1 Consensus size: 29
7312 GGAGGTTCGG
* * * * **
7322 GGGTAAAAATGAAATTCTTAGAAATTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA
* *
7351 GGGTCAAAAATGGCATTTTTGGAAGGTT-A
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCA
* *
7380 AGGTAAAAATGGAATATTTGGAAGTTTCA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA
7409 GGGTAAAAAAT-GAGATTTTTGGAAG-TTCGA
1 GGGT-AAAAATGGA-ATTTTTGGAAGTTTC-A
* *
7439 GGGTAAAAATGGGATTTTTGGAAGTTTTA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA
* * **
7468 TGGTTAAAAAT-AAGATTTTTGGAAGTTTGG
1 -GGGTAAAAATGGA-ATTTTTGGAAGTTTCA
**
7498 GGGT-AAAATGGAATTTTTGGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA
**
7526 GGGTTAAAAATAGG-ATTTTTGGAAGTTTTG
1 GGG-TAAAAAT-GGAATTTTTGGAAGTTTCA
* *
7556 GGGTCAAAAATAGG-GTTTTTGGAAG-TTCGG
1 GGGT-AAAAAT-GGAATTTTTGGAAGTTTC-A
7586 GGGTAAAAATGGAATTTTTGGAAGTTTC-
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA
*
7614 GGGTAAAAATGGGATTTTTGGAAGTTTC-
1 GGGTAAAAATGGAATTTTTGGAAGTTTCA
**
7642 GAGGTCAGAAAAAAG-ATTTTTGGAAG-TTCGA
1 G-GGT-A-AAAATGGAATTTTTGGAAGTTTC-A
7673 GGGTAAAAATGGAATTTTTGGACAGTTT-A
1 GGGTAAAAATGGAATTTTTGGA-AGTTTCA
7702 GGG
1 GGG
7705 ACCTCTAGGG
Statistics
Matches: 298, Mismatches: 31, Indels: 50
0.79 0.08 0.13
Matches are distributed among these distances:
28 78 0.26
29 78 0.26
30 132 0.44
31 10 0.03
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCA
Found at i:7437 original size:117 final size:113
Alignment explanation
Indices: 7298--7700 Score: 391
Period size: 117 Copynumber: 3.4 Consensus size: 113
7288 TTTGAGGTCG
* * * * * *
7298 AAAATAGAGATTTTGGAGGTTCGGGGGTAAAAATGAAATTCTTAGAAATTTTGGGGTCAAAAATG
1 AAAATAGA-TTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGT-AAAAATG
* * *
7363 GCATTTTTGGAAGGTTAAGGTAAAAATGGAATATTTGGAAGTTTCAGGGTAA
64 G-ATTTTTGGAAGTTTAGGGTAAAAATGGAATTTTTGGAAGTTTC-GGGTAA
** * *
7415 AAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTATGGTTAAAAATA
1 AAAAT-AGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGAAGTTTT-GGGGTAAAAAT-
* * * *
7480 AGATTTTTGGAAGTTTGGGGGT-AAAATGGAATTTTTGGAAGTTTTGGGGTTA
63 GGATTTTTGGAAGTTT-AGGGTAAAAATGGAATTTTTGGAAG-TTTCGGGTAA
* ** **
7532 AAAATAGGATTTTTGGAAGTTTTG-GGGTCAAAAAT-AGGGTTTTTGGAAGTTCGGGGGTAAAAA
1 AAAATA-GATTTTTGGAAG-TTCGAGGGT-AAAAATGA-AATTTTTGGAAGTTTTGGGGTAAAAA
* *
7595 TGGAATTTTTGGAAGTTTCGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTCAGA
62 TGG-ATTTTTGGAAGTTTAGGGTAAAAATGGAATTTTTGGAAGTTTCG-GGT-A-A
*
7651 AAAA-AGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGACAGTTT
1 AAAATAGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA-AGTTT
7701 AGGGACCTCT
Statistics
Matches: 235, Mismatches: 34, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
116 27 0.11
117 167 0.71
118 36 0.15
119 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (113 bp):
AAAATAGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGTAAAAATGGA
TTTTTGGAAGTTTAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGTAA
Found at i:7603 original size:59 final size:58
Alignment explanation
Indices: 7298--7700 Score: 333
Period size: 58 Copynumber: 6.9 Consensus size: 58
7288 TTTGAGGTCG
* * ** * * * *
7298 AAAATAGAGA-TTTTGGAGGTTCGGGGGTAAAAATGAAATTCTTAGAAATTT-TGGGGTCA
1 AAAAT-GAGATTTTTGGAAGTT-TGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGGT-A
* ** * * *
7357 AAAATG-GCATTTTTGGAAGGTTAAGGTAAAAATGGAATATTTGGAAGTTTC-AGGGTAA
1 AAAATGAG-ATTTTTGGAAGTTTGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGGT-A
* *** *
7415 AAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTATGGTTA
1 AAAATGAGATTTTTGGAAGTTTG-GGGTAAAAATGGGATTTTTGGAAGTTTCGGGGGTA
* * * *
7474 AAAATAAGATTTTTGGAAGTTTGGGGGT-AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGAGATTTTTGGAAGTTT-GGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGGTA
7532 AAAAT-AGGATTTTTGGAAGTTTTGGGGTCAAAAATAGGG-TTTTTGGAAG-TTCGGGGGTA
1 AAAATGA-GATTTTTGGAAG-TTTGGGGT-AAAAAT-GGGATTTTTGGAAGTTTCGGGGGTA
* *
7591 AAAATG-GAATTTTTGGAAGTTTCGGGTAAAAATGGGATTTTTGGAAGTTTC-GAGGTCA
1 AAAATGAG-ATTTTTGGAAGTTTGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGGT-A
* * *
7649 GAAAA-AAGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGACAGTTT
1 -AAAATGAGATTTTTGGAAGTTTG-GGGTAAAAATGGGATTTTTGGA-AGTTT
7701 AGGGACCTCT
Statistics
Matches: 288, Mismatches: 35, Indels: 41
0.79 0.10 0.11
Matches are distributed among these distances:
56 3 0.01
57 22 0.08
58 120 0.42
59 117 0.41
60 24 0.08
61 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (58 bp):
AAAATGAGATTTTTGGAAGTTTGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGGTA
Done.