Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014007.1 Kokia drynarioides strain JFW-HI SEQ_129038, 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: 8039
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:2075 original size:12 final size:12
Alignment explanation
Indices: 2058--2083 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2048 TTCCTCGCTT
2058 CCCACTATACAA
1 CCCACTATACAA
2070 CCCACTATACAA
1 CCCACTATACAA
2082 CC
1 CC
2084 AAACAAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (12 bp):
CCCACTATACAA
Found at i:3908 original size:29 final size:28
Alignment explanation
Indices: 3859--4344 Score: 215
Period size: 29 Copynumber: 16.6 Consensus size: 28
3849 ACCCGGGGAT
**
3859 AAAATGGCAATTTTTAAAAGTTCAGTGTCA
1 AAAATGG-AATTTTTGGAAGTTCAG-GTCA
* * *
3889 CAAATGGAATTTTTGGAAGTTCGGGGCTA
1 AAAATGGAATTTTTGGAAGTTCAGGTC-A
3918 AAAATGGAATTTTTGGAAGTTTCA-GTCA
1 AAAATGGAATTTTTGGAAG-TTCAGGTCA
*
3946 AAAATGGGATTTTTGGAAGTTCGGAGGT-A
1 AAAATGGAATTTTTGGAAGTTC--AGGTCA
* * **
3975 AAAATGGTAA-TTTTGAGAAAATTTGAGGGGA
1 AAAATGG-AATTTTTG-G--AAGTTCAGGTCA
* * * * ***
4006 AAAATGGAAATTTT-AAACATTTAGGGGT
1 AAAATGGAATTTTTGGAA-GTTCAGGTCA
* *
4034 AAAAGGGTAA-TTTT-GAGAGTTTCGAGGTCG
1 AAAATGG-AATTTTTGGA-AG-TTC-AGGTCA
* ** * ***
4064 AAAATGGAGTTTTT-GAACATCTGGGGGT
1 AAAATGGAATTTTTGGAAGTTC-AGGTCA
** *
4092 AAAATGGTAA-TTTTAAAAGTTTCAGTGTTA
1 AAAATGG-AATTTTTGGAAG-TTCAG-GTCA
* *
4122 AAAATGGAATTTTTGGAAGTTCGGGGCTA
1 AAAATGGAATTTTTGGAAGTTCAGGTC-A
* **
4151 AAAATAGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG--TTCAGGTCA
* *
4181 AAAAT-GAGATTTTTGGAGGTTCGGGGGT-A
1 AAAATGGA-ATTTTTGGAAGTTC--AGGTCA
* *
4210 AAAATGGAATTCTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTC-AGGTCA
4240 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
1 AAAATGGAATTTTTGGAAGTTC-A-GGTCA
* *
4269 AAAATGGAATTTTTTGAAGTTTCGGGATCA
1 AAAATGGAATTTTTGGAAG-TTCAGG-TCA
4299 AAAATAGG-ATTTTTGGAAGTTCAGGGGT-A
1 AAAAT-GGAATTTTTGGAAGTTCA--GGTCA
4328 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
4345 TATTTTAGGG
Statistics
Matches: 358, Mismatches: 59, Indels: 79
0.72 0.12 0.16
Matches are distributed among these distances:
27 5 0.01
28 61 0.17
29 149 0.42
30 117 0.33
31 22 0.06
32 4 0.01
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCAGGTCA
Found at i:4142 original size:30 final size:30
Alignment explanation
Indices: 4108--4344 Score: 265
Period size: 29 Copynumber: 8.0 Consensus size: 30
4098 GTAATTTTAA
* *
4108 AAGTTTCAGTGTTAAAAATGGAATTTTTGG
1 AAGTTTCGGGGTTAAAAATGGAATTTTTGG
* *
4138 AAG-TTCGGGGCTAAAAATAGAATTTTTGG
1 AAGTTTCGGGGTTAAAAATGGAATTTTTGG
* *
4167 AAGTTTTGGGGTCAAAAAT-GAGATTTTTGG
1 AAGTTTCGGGGTTAAAAATGGA-ATTTTTGG
* * *
4197 -AGGTTCGGGGGTAAAAATGGAATTCTTGG
1 AAGTTTCGGGGTTAAAAATGGAATTTTTGG
*
4226 AAGTTTCGGGGTCAAAAATGGAATTTTTGG
1 AAGTTTCGGGGTTAAAAATGGAATTTTTGG
*
4256 AAG-TTCGAGGG-TAAAAATGGAATTTTTTG
1 AAGTTTCG-GGGTTAAAAATGGAATTTTTGG
* *
4285 AAGTTTCGGGATCAAAAATAGG-ATTTTTGG
1 AAGTTTCGGGGTTAAAAAT-GGAATTTTTGG
4315 AAG-TTCAGGGG-TAAAAATGGAATTTTTGG
1 AAGTTTC-GGGGTTAAAAATGGAATTTTTGG
4344 A
1 A
4345 TATTTTAGGG
Statistics
Matches: 174, Mismatches: 23, Indels: 21
0.80 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 91 0.52
30 79 0.45
31 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.33
Consensus pattern (30 bp):
AAGTTTCGGGGTTAAAAATGGAATTTTTGG
Found at i:4193 original size:59 final size:58
Alignment explanation
Indices: 3859--4344 Score: 424
Period size: 59 Copynumber: 8.3 Consensus size: 58
3849 ACCCGGGGAT
** * * *
3859 AAAATGGCAATTTTTAAAAG-TTCAGTGTCACAAATGGAATTTTTGGAAGTTCGGGGCTA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGG-TA
* *
3918 AAAATGGAATTTTTGGAAGTTTC--AGTCAAAAATGGGATTTTTGGAAGTTCGGAGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGG-GGTA
* * * ** * *
3975 AAAATGGTAA-TTTTGAGAAAATTT-GAGGG-GAAAAATGGAAATTTTAAACATTTAGGGGT-
1 AAAATGG-AATTTTTG-G-AAGTTTCG-GGGTCAAAAATGGAATTTTTGGA-AGTTCGGGGTA
* * * * * *
4034 AAAAGGGTAA-TTTT-GAGAGTTTCGAGGTCGAAAATGGAGTTTTT-GAACATCTGGGGGT-
1 AAAATGG-AATTTTTGGA-AGTTTCGGGGTCAAAAATGGAATTTTTGGAA-GT-TCGGGGTA
** * * *
4092 AAAATGGTAA-TTTTAAAAGTTTCAGTGTTAAAAATGGAATTTTTGGAAGTTCGGGGCTA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGG-TA
* * *
4151 AAAATAGAATTTTTGGAAGTTTTGGGGTCAAAAAT-GAGATTTTTGGAGGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGA-ATTTTTGGAAGTTC-GGGGTA
*
4210 AAAATGGAATTCTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCG-GGGTA
* *
4269 AAAATGGAATTTTTTGAAGTTTCGGGATCAAAAATAGG-ATTTTTGGAAGTTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAAT-GGAATTTTTGGAAGTTC-GGGGTA
4328 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
4345 TATTTTAGGG
Statistics
Matches: 352, Mismatches: 50, Indels: 50
0.78 0.11 0.11
Matches are distributed among these distances:
56 2 0.01
57 54 0.15
58 75 0.21
59 189 0.54
60 26 0.07
61 6 0.02
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGTA
Found at i:4344 original size:118 final size:117
Alignment explanation
Indices: 3859--4344 Score: 478
Period size: 118 Copynumber: 4.2 Consensus size: 117
3849 ACCCGGGGAT
* ** * *
3859 AAAATGGCAATTTTTAAAAG-TTCAGTGTCACAAATGGAATTTTTGGAAGTTCGGGGCTAAAAAT
1 AAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGCTAAAAAT
* *
3923 GGAATTTTTGGAAGTTTC-AGTCAAAAATGGGATTTTTGGAAGTTCGGAGGTA
66 GGAATTTTTGGAAGTTTCGGGTCAAAAAT-GGATTTTTGGAAGTTCGGGGGTA
* * * * ** * *
3975 AAAATGGTAA-TTTTGAGAAAATTTGAGGG-GAAAAATGGAAATTTTAAACATTTAGGGG-T-AA
1 AAAATGGTAATTTTTG-G-AAGTTTCAGGGTCAAAAATGGAATTTTTGGA-AGTTCGGGGCTAAA
* * **
4036 AAGGGTAA-TTTT-GAGAGTTTCGAGGTCGAAAATGGAGTTTTT-GAACATCTGGGGGT-
63 AATGG-AATTTTTGGA-AGTTTCG-GGTCAAAAATGGA-TTTTTGGAAGTTC-GGGGGTA
** * *
4092 AAAATGGTAA-TTTTAAAAGTTTCAGTGTTAAAAATGGAATTTTTGGAAGTTCGGGGCTAAAAAT
1 AAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGCTAAAAAT
* * *
4156 AGAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAGGTTCGGGGGTA
66 GGAATTTTTGGAAG-TTTCGGGTCAAAAATG-GATTTTTGGAAGTTCGGGGGTA
* *
4210 AAAATGG-AATTCTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGG-TAAAAA
1 AAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCG-GGGCTAAAAA
* *
4273 TGGAATTTTTTGAAGTTTCGGGATCAAAAATAGGATTTTTGGAAGTTCAGGGGTA
65 TGGAATTTTTGGAAGTTTCGGG-TCAAAAAT-GGATTTTTGGAAGTTCGGGGGTA
4328 AAAATGG-AATTTTTGGA
1 AAAATGGTAATTTTTGGA
4345 TATTTTAGGG
Statistics
Matches: 298, Mismatches: 49, Indels: 44
0.76 0.13 0.11
Matches are distributed among these distances:
115 21 0.07
116 43 0.14
117 81 0.27
118 149 0.50
119 4 0.01
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGCTAAAAAT
GGAATTTTTGGAAGTTTCGGGTCAAAAATGGATTTTTGGAAGTTCGGGGGTA
Found at i:5462 original size:3 final size:3
Alignment explanation
Indices: 5402--5444 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
5392 TTTCATTTTT
*
5402 TTA TTA TTA TTA TTCA TTA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
5445 AGAAAATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:6268 original size:5 final size:6
Alignment explanation
Indices: 6233--6302 Score: 70
Period size: 6 Copynumber: 11.3 Consensus size: 6
6223 TATAATAATC
* * *
6233 TTAAAT TTAGAAA ATAAAT TTAAAC TTAAA- TTAAAT TTAAATT ATTAAAT
1 TTAAAT TTA-AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T -TTAAAT
*
6283 TTATAT TTAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TT
6303 TTAAACAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
5 5 0.09
6 37 0.70
7 6 0.11
8 5 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:6292 original size:20 final size:19
Alignment explanation
Indices: 6258--6295 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
6248 AAATTTAAAC
6258 TTAAATTAAATTTAAATTA
1 TTAAATTAAATTTAAATTA
*
6277 TTAAATTTATATTTAAATT
1 TTAAA-TTAAATTTAAATT
6296 TAAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAATTAAATTTAAATTA
Done.