Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008002.1 Kokia drynarioides strain JFW-HI SEQ_122654, 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: 81347
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:4987 original size:16 final size:16
Alignment explanation
Indices: 4968--5009 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4958 TAAAACTATT
4968 AAATATTAAATTAAAA
1 AAATATTAAATTAAAA
* *
4984 AAATATAAATATTTAAA
1 AAATATTAA-ATTAAAA
5001 AAA-ATTAAA
1 AAATATTAAA
5010 AAATAATACG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.05
16 12 0.55
17 9 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATATTAAATTAAAA
Found at i:12231 original size:15 final size:16
Alignment explanation
Indices: 12201--12239 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
12191 TAATAAAAAT
12201 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
12218 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
12233 ATAATTT
1 ATAATTT
12240 TTAAATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:12232 original size:24 final size:23
Alignment explanation
Indices: 12172--12245 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 23
12162 GGTTTGAATT
**
12172 AAATTATATATTTTTATTATAATA
1 AAATT-TATATTTTTATTATTTTA
* *
12196 AAA-ATATAATTTTATTATTTTA
1 AAATTTATATTTTTATTATTTTA
* *
12218 ATAATTTATATTTTTATAATTTTT
1 A-AATTTATATTTTTATTATTTTA
12242 AAAT
1 AAAT
12246 GATTAAATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
22 16 0.40
23 5 0.12
24 19 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATTTATATTTTTATTATTTTA
Found at i:12272 original size:31 final size:31
Alignment explanation
Indices: 12229--12299 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
12219 TAATTTATAT
* * *
12229 TTTTAT-AATTTTTAAATGATTAAATTAAAA
1 TTTTATCATTTTTTAAAAGATTAAAGTAAAA
*
12259 TTTTATCATTTTTTAAAAGATTAAAGTATAA
1 TTTTATCATTTTTTAAAAGATTAAAGTAAAA
12290 TTTTATCATT
1 TTTTATCATT
12300 ATTAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 6 0.17
31 30 0.83
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (31 bp):
TTTTATCATTTTTTAAAAGATTAAAGTAAAA
Found at i:12303 original size:22 final size:22
Alignment explanation
Indices: 12278--12323 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
12268 TTTTTAAAAG
* *
12278 ATTAAAGTATAATTTTATCATT
1 ATTAAAGTAAAATTTTATAATT
**
12300 ATTAATTTAAAATTTTATAATT
1 ATTAAAGTAAAATTTTATAATT
12322 AT
1 AT
12324 AAAAAACGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTAAAGTAAAATTTTATAATT
Found at i:38548 original size:29 final size:31
Alignment explanation
Indices: 38493--38552 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
38483 GGTGACCAAT
38493 TTATTATCAATTGATAACATTCGTAATCAAA
1 TTATTATCAATTGATAACATTCGTAATCAAA
38524 TTATTA-CAATTGA-AACA-TCGATAATCAAA
1 TTATTATCAATTGATAACATTCG-TAATCAAA
38553 ACGTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 3 0.11
29 12 0.43
30 7 0.25
31 6 0.21
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (31 bp):
TTATTATCAATTGATAACATTCGTAATCAAA
Found at i:40219 original size:12 final size:12
Alignment explanation
Indices: 40202--40226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40192 TTTACAATAA
40202 AAAAAAAAAAAG
1 AAAAAAAAAAAG
40214 AAAAAAAAAAAG
1 AAAAAAAAAAAG
40226 A
1 A
40227 GTAAGGGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:55121 original size:3 final size:3
Alignment explanation
Indices: 55113--55141 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55103 TAAATAGAGA
55113 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55142 ATGAGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:62972 original size:3 final size:3
Alignment explanation
Indices: 62964--62990 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
62954 GATGAATTTT
62964 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
62991 AATGAGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:74027 original size:15 final size:15
Alignment explanation
Indices: 74007--74037 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
73997 TTTGCGCATA
*
74007 AATTTTCGGTTATTG
1 AATTTTCAGTTATTG
74022 AATTTTCAGTTATTG
1 AATTTTCAGTTATTG
74037 A
1 A
74038 TTTGAAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (15 bp):
AATTTTCAGTTATTG
Found at i:80096 original size:20 final size:20
Alignment explanation
Indices: 80058--80096 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
80048 AGAATTGTTT
*
80058 GGAATGTGTTGTTTGGAGCA
1 GGAATGTGTTGTTTAGAGCA
80078 GGAATGTTGTTG-TTAGAGC
1 GGAATG-TGTTGTTTAGAGC
80097 CACTCAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.21, C:0.05, G:0.38, T:0.36
Consensus pattern (20 bp):
GGAATGTGTTGTTTAGAGCA
Done.