Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009183.1 Kokia drynarioides strain JFW-HI SEQ_123888, 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: 71521
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 199 characters in sequence are not A, C, G, or T
Found at i:5857 original size:116 final size:116
Alignment explanation
Indices: 5653--5882 Score: 444
Period size: 116 Copynumber: 2.0 Consensus size: 116
5643 AGAAAACGTT
5653 AATGGTTCAAAAATCATTCTTTTCAGATATAAATGAATCACTTTCAGAAACCCAACCCGAAATTT
1 AATGGTTCAAAAATCATTCTTTTCAGATATAAATGAATCACTTTCAGAAACCCAACCCGAAATTT
5718 CTTTCTTTTTTTTCCCTTGGAGGAGTAATAGATTGAGAAAGAGAGGACCCC
66 CTTTCTTTTTTTTCCCTTGGAGGAGTAATAGATTGAGAAAGAGAGGACCCC
5769 AATGGTTCAAAAATCATTCTTTTCAGATATAAATGAATCAAC-TTCAGAAACCCAACCCGAAATT
1 AATGGTTCAAAAATCATTCTTTTCAGATATAAATGAATC-ACTTTCAGAAACCCAACCCGAAATT
5833 TCTTTCTTTTTTTTCCCTTGGAGGAGTAATAGATTGAGAAAGAGAGGACC
65 TCTTTCTTTTTTTTCCCTTGGAGGAGTAATAGATTGAGAAAGAGAGGACC
5883 TTATAAAGAT
Statistics
Matches: 113, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
116 111 0.98
117 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (116 bp):
AATGGTTCAAAAATCATTCTTTTCAGATATAAATGAATCACTTTCAGAAACCCAACCCGAAATTT
CTTTCTTTTTTTTCCCTTGGAGGAGTAATAGATTGAGAAAGAGAGGACCCC
Found at i:19265 original size:75 final size:75
Alignment explanation
Indices: 19174--19325 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
19164 TCCACCTCTT
* * *
19174 GGTTTATAATAATCTAACTACTAATAAAACGGATTTTTGGAAAATGTAAGTGCGTAACTTTTTTT
1 GGTTTATAATAATCTAACTACTAATAAAACGGATTTTTGAAAAATGTAAGTACGTAACTTCTTTT
19239 TGAGACATAA
66 TGAGACATAA
* * *
19249 GGTTTATCATAATCTAACTACTAATAAAATGGATTTTTGAAAAATGTAAGTACGTTACTTCTTTT
1 GGTTTATAATAATCTAACTACTAATAAAACGGATTTTTGAAAAATGTAAGTACGTAACTTCTTTT
*
19314 TGGGACATAA
66 TGAGACATAA
19324 GG
1 GG
19326 CTTAGTAGCT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (75 bp):
GGTTTATAATAATCTAACTACTAATAAAACGGATTTTTGAAAAATGTAAGTACGTAACTTCTTTT
TGAGACATAA
Found at i:30299 original size:16 final size:16
Alignment explanation
Indices: 30278--30308 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30268 CATATTAGAG
30278 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
30294 CATATACATTTGAAA
1 CATATAAATTTGAAA
30309 ACTTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:30502 original size:20 final size:19
Alignment explanation
Indices: 30454--30490 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
30444 ATTTAAAAAA
30454 TATAAAT-TTTAAAATTTT
1 TATAAATATTTAAAATTTT
30472 TATAAATATTT-AAATTTT
1 TATAAATATTTAAAATTTT
30490 T
1 T
30491 TGAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAAAATTTT
Found at i:38938 original size:18 final size:18
Alignment explanation
Indices: 38915--38950 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38905 AAATGACACA
*
38915 TGAAATTGATTAAACGAC
1 TGAAATGGATTAAACGAC
38933 TGAAATGGATTAAACGAC
1 TGAAATGGATTAAACGAC
38951 AATCTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (18 bp):
TGAAATGGATTAAACGAC
Found at i:43018 original size:13 final size:13
Alignment explanation
Indices: 43002--43026 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42992 CTTAAATAAT
43002 TCACTTATGAAAA
1 TCACTTATGAAAA
43015 TCACTTATGAAA
1 TCACTTATGAAA
43027 CCAATTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TCACTTATGAAAA
Found at i:46282 original size:34 final size:34
Alignment explanation
Indices: 46239--46309 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
46229 TAATAACTAT
46239 AAAAAATTATAGAAAACTA-TATAAAAATGATAAA
1 AAAAAATTAT-GAAAACTATTATAAAAATGATAAA
* * * *
46273 AAAAAATTATTAAAAGTATTATAAATATTATAAA
1 AAAAAATTATGAAAACTATTATAAAAATGATAAA
46307 AAA
1 AAA
46310 TTTATTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 6 0.19
34 26 0.81
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (34 bp):
AAAAAATTATGAAAACTATTATAAAAATGATAAA
Found at i:52623 original size:3 final size:3
Alignment explanation
Indices: 52617--52656 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
52607 CAACAATAGT
52617 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52657 CCAAACAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:57544 original size:6 final size:6
Alignment explanation
Indices: 57533--57560 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
57523 TGAGTAGAGC
57533 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
57561 TCTTCTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:60902 original size:21 final size:20
Alignment explanation
Indices: 60873--60912 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
60863 ATATCAATTT
60873 TAATATTTTTAATAATTTTTG
1 TAATATTTTTAAT-ATTTTTG
* *
60894 TAATTTTTTTAGTATTTTT
1 TAATATTTTTAATATTTTT
60913 AAGAATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TAATATTTTTAATATTTTTG
Found at i:60988 original size:20 final size:19
Alignment explanation
Indices: 60969--61011 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
60959 TCATATTAAT
60969 TTTA-TAAATTTTTATATAA
1 TTTATTAAATTTTT-TATAA
*
60988 TTTATTAGATTTTTTATAAA
1 TTTATTAAATTTTTTAT-AA
61008 TTTA
1 TTTA
61012 GATCAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTATTAAATTTTTTATAA
Found at i:61439 original size:3 final size:3
Alignment explanation
Indices: 61431--61460 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
61421 ACGTGGCCCA
61431 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
61461 GATTCTTACA
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:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:66108 original size:28 final size:30
Alignment explanation
Indices: 66073--66136 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
66063 TTAAGATTTT
**
66073 TAAAAAA-TAAATTTTTAATTTT-T-AAAA
1 TAAAAAATTAAATTTCAAATTTTATAAAAA
66100 TAAAGAAATTAAATTTCAAATTTTATAAAAA
1 TAAA-AAATTAAATTTCAAATTTTATAAAAA
66131 TAAAAA
1 TAAAAA
66137 GAGTTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 4 0.13
28 3 0.10
29 13 0.42
30 3 0.10
31 8 0.26
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
TAAAAAATTAAATTTCAAATTTTATAAAAA
Found at i:68340 original size:23 final size:23
Alignment explanation
Indices: 68278--68340 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
68268 CGTTAGTATC
**
68278 AAACAACTATTGTTTTTAGGTAA
1 AAACAACTATTCCTTTTAGGTAA
**
68301 AAACAACTATTGTTTTTAGGTAA
1 AAACAACTATTCCTTTTAGGTAA
68324 AAACAACT-TTACCTTTT
1 AAACAACTATT-CCTTTT
68341 CACTTGTACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 2 0.05
23 35 0.95
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (23 bp):
AAACAACTATTCCTTTTAGGTAA
Found at i:68340 original size:24 final size:23
Alignment explanation
Indices: 68278--68331 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
68268 CGTTAGTATC
*
68278 AAACAACTATTGTTTTTAGGTAA
1 AAACAACTATTCTTTTTAGGTAA
*
68301 AAACAACTATTGTTTTTAGGTAA
1 AAACAACTATTCTTTTTAGGTAA
68324 AAACAACT
1 AAACAACT
68332 TTACCTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (23 bp):
AAACAACTATTCTTTTTAGGTAA
Done.