Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010982.1 Kokia drynarioides strain JFW-HI SEQ_125952, 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: 5973
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:3428 original size:3 final size:3
Alignment explanation
Indices: 3422--3451 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3412 CATCATCCTC
3422 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3452 GTTGTTGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3456 original size:3 final size:3
Alignment explanation
Indices: 3450--3521 Score: 101
Period size: 3 Copynumber: 24.3 Consensus size: 3
3440 ATTATTATTA
* *
3450 TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG TTG TTG TTG TTA
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* *
3498 TT- TTG TTG CTG CTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
3522 CATTGTTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.03, C:0.03, G:0.29, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:3778 original size:5 final size:5
Alignment explanation
Indices: 3764--3797 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
3754 AAGTATGCTA
3764 TTTTC TTTTTC TTTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
3798 GCCATGGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:4113 original size:3 final size:3
Alignment explanation
Indices: 4105--4191 Score: 149
Period size: 3 Copynumber: 29.3 Consensus size: 3
4095 NNNNNNNNNN
4105 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* *
4153 TTG TTG TTG TTG TTA TT- TTG TTG TTG CTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
4192 CATTGTTATT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.03
3 78 0.98
ACGTcount: A:0.01, C:0.01, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:4392 original size:17 final size:19
Alignment explanation
Indices: 4370--4404 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4360 TTTTTAAAAT
4370 AAAAA-TTTG-TTTTTTAG
1 AAAAATTTTGATTTTTTAG
4387 AAAAATTTTGATTTTTTA
1 AAAAATTTTGATTTTTTA
4405 ACTATTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (19 bp):
AAAAATTTTGATTTTTTAG
Found at i:4732 original size:152 final size:148
Alignment explanation
Indices: 4361--4752 Score: 515
Period size: 152 Copynumber: 2.6 Consensus size: 148
4351 AAGTTTAGAT
* * *
4361 TTTTAAA-ATAAAAATTTG-TTTTTTAGAAAAATTTTGA-TTTTTTAACTATTTTGAAATAAAAG
1 TTTTAAAGA-AAAAATTTGAATTTTTAAAAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAG
** * * *
4423 TTCGGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAAGAAAGTTTATATTTTTAAATATAA
65 TTTAGATTTTTAAGTAAAGTAGTGATTTTCTTAAAAAAAAAGAAAGTTTAGATTTTTAAATATAA
*
4488 AAATCTGGTTTTTTAGTTA
130 AAATCTGGTTTTTTAGTGA
* * *
4507 TTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAG
1 TTTTAAAGAAAAAATTTGAATTTTTAAA-AAAATTTTGATTTTTTTAACTATTTCGAAATAAAAG
* *
4572 TTTAGATTTTTAACTAAAGTAGTAATTTTCATTAAAAAAAGAAAGAAAG-TTAGATTTTTAAAAT
65 TTTAGATTTTTAAGTAAAGTAGTGATTTTC-TT-AAAAAA-AAAGAAAGTTTAGATTTTT-AAAT
*
4636 ATAAAAAT-TTGTTTTTTAGTGA
126 ATAAAAATCTGGTTTTTTAGTGA
4658 TTTTAAAGAAAAAATTTGAATTTTTAAACAAAATTTTGATTTTTTTTAACTATTTCGAAATAAAA
1 TTTTAAAGAAAAAATTTGAATTTTTAAA-AAAATTTTGA-TTTTTTTAACTATTTCGAAATAAAA
* * *
4723 ATTTTGATTTTGAAGTAAAGTAGTGATTTT
64 GTTTAGATTTTTAAGTAAAGTAGTGATTTT
4753 GTTTTAATCA
Statistics
Matches: 213, Mismatches: 24, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
146 14 0.07
147 8 0.04
148 9 0.04
149 49 0.23
150 2 0.01
151 61 0.29
152 70 0.33
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (148 bp):
TTTTAAAGAAAAAATTTGAATTTTTAAAAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGT
TTAGATTTTTAAGTAAAGTAGTGATTTTCTTAAAAAAAAAGAAAGTTTAGATTTTTAAATATAAA
AATCTGGTTTTTTAGTGA
Done.