Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007716.1 Kokia drynarioides strain JFW-HI SEQ_122349, 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: 33569
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:4244 original size:30 final size:30
Alignment explanation
Indices: 4201--4344 Score: 134
Period size: 30 Copynumber: 4.8 Consensus size: 30
4191 TCAAATAATT
4201 TTTTTTGGAAAGTTTGGGGGTTAAATCCT-AA
1 TTTTTTGG-AAGTTTGGGGGTTAAAT-CTAAA
* * *
4232 TTTTTTGGAAGTTTAGGGGTCAAATCTGAA
1 TTTTTTGGAAGTTTGGGGGTTAAATCTAAA
* ** *
4262 TTTTTGGGAAG-TTAAGGGTCAAATCTAAA
1 TTTTTTGGAAGTTTGGGGGTTAAATCTAAA
* * *
4291 TTTTTGGGAAGTTCGAGGGTCT-AATCTAAA
1 TTTTTTGGAAGTTTGGGGGT-TAAATCTAAA
4321 -TTTTTGGATAGTTTGGGGGTTAAA
1 TTTTTTGGA-AGTTTGGGGGTTAAA
4345 ATGTAATTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
29 37 0.38
30 52 0.54
31 8 0.08
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.40
Consensus pattern (30 bp):
TTTTTTGGAAGTTTGGGGGTTAAATCTAAA
Found at i:6464 original size:80 final size:80
Alignment explanation
Indices: 6273--6493 Score: 243
Period size: 80 Copynumber: 2.8 Consensus size: 80
6263 AATGTAAGGG
* * *
6273 CCCTCCGATAGCCAAGATCCTGCATATGTTGC-AGATTCTTGACAGCTTGTGTGAGCAGCATCGT
1 CCCTCCGATGGCTAAGATCCTACATATGTTGCGA-ATTCTTGACAGCTTGTGTGAGCAGCATCGT
*
6337 GAGTGGATAAAGTGAA
65 GAGTGGATAAAATGAA
*
6353 CCCTCCGATGGCTAAGATCCTACATACGTTGCGAATTCTTGACAGCTTGTGTGAGCTA-CATCGT
1 CCCTCCGATGGCTAAGATCCTACATATGTTGCGAATTCTTGACAGCTTGTGTGAGC-AGCATCGT
*
6417 GAGTGGATAAAATGGA
65 GAGTGGATAAAATGAA
** * * * * ** *
6433 CTGTATCGATGGCTGAG-T-CTGTCATATGTTGCGGATTCTCAACAGCTTGTATGAGCAGCAT
1 CCCT-CCGATGGCTAAGATCCT-ACATATGTTGCGAATTCTTGACAGCTTGTGTGAGCAGCAT
6494 TGTATACTGG
Statistics
Matches: 120, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
79 3 0.03
80 105 0.88
81 12 0.10
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.29
Consensus pattern (80 bp):
CCCTCCGATGGCTAAGATCCTACATATGTTGCGAATTCTTGACAGCTTGTGTGAGCAGCATCGTG
AGTGGATAAAATGAA
Found at i:7219 original size:4 final size:4
Alignment explanation
Indices: 7205--7354 Score: 86
Period size: 4 Copynumber: 36.5 Consensus size: 4
7195 AATTTAAAAA
* * * * * *
7205 TATT TATTT TATT TATT TAAT TATT TGTTT TATT TAAT TAGT TAAT TATA
1 TATT TA-TT TATT TATT TATT TATT T-ATT TATT TATT TATT TATT TATT
* * * * * *
7255 TATA TATA TATAT T-TT TAGT TAAT TATT TATTT TATT TAGT TAAT TATT
1 TATT TATT TAT-T TATT TATT TATT TATT TA-TT TATT TATT TATT TATT
* * * * * *
7304 TAGT TATT TATTT TGTT TATT TTTT TATT CAGT TATT TATT TACT TATT
1 TATT TATT TA-TT TATT TATT TATT TATT TATT TATT TATT TATT TATT
7353 TA
1 TA
7355 CTTAGTTAAA
Statistics
Matches: 112, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
3 2 0.02
4 95 0.85
5 15 0.13
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (4 bp):
TATT
Found at i:7322 original size:29 final size:29
Alignment explanation
Indices: 7278--7345 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
7268 TTTTAGTTAA
*
7278 TTATTTATTTTATTTAGTTAATTATTTAG
1 TTATTTATTTTATTTAGTTAATTATTCAG
* * **
7307 TTATTTATTTTGTTTATTTTTTTATTCAG
1 TTATTTATTTTATTTAGTTAATTATTCAG
7336 TTATTTATTT
1 TTATTTATTT
7346 ACTTATTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.01, G:0.06, T:0.71
Consensus pattern (29 bp):
TTATTTATTTTATTTAGTTAATTATTCAG
Found at i:9721 original size:15 final size:15
Alignment explanation
Indices: 9690--9727 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
9680 TTAATAAAAA
9690 TAAATGTAACAATATT
1 TAAAT-TAACAATATT
9706 TAAATTAACGAA-ATT
1 TAAATTAAC-AATATT
9721 TAAATTA
1 TAAATTA
9728 TCATATTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (15 bp):
TAAATTAACAATATT
Found at i:14131 original size:22 final size:23
Alignment explanation
Indices: 14103--14149 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
14093 TTAAAGCATA
* *
14103 TAAGTATTTCATAT-ATTAATAT
1 TAAGTATTTAATATAATTAAGAT
14125 TAAGTATTTAATATAATTAAGAT
1 TAAGTATTTAATATAATTAAGAT
14148 TA
1 TA
14150 TATAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (23 bp):
TAAGTATTTAATATAATTAAGAT
Found at i:14149 original size:23 final size:22
Alignment explanation
Indices: 14089--14149 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
14079 ATTAAATTTT
*
14089 TATATTAAAGCATATAAGTATTTCA
1 TATATT-AAG-AT-TAAGTATTTAA
*
14114 TATATTAATATTAAGTATTTAA
1 TATATTAAGATTAAGTATTTAA
14136 TATAATTAAGATTA
1 TAT-ATTAAGATTA
14150 TATAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 13 0.41
23 11 0.34
24 2 0.06
25 6 0.19
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (22 bp):
TATATTAAGATTAAGTATTTAA
Found at i:26534 original size:4 final size:4
Alignment explanation
Indices: 26518--26582 Score: 121
Period size: 4 Copynumber: 16.2 Consensus size: 4
26508 TATCATGTAC
*
26518 ACAT ACGT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
26566 ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT A
26583 TTAGTAAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.49, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:27489 original size:3 final size:3
Alignment explanation
Indices: 27478--27511 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
27468 TAATAAGCAC
*
27478 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
27512 GATGATGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:27539 original size:9 final size:9
Alignment explanation
Indices: 27478--27540 Score: 54
Period size: 9 Copynumber: 7.0 Consensus size: 9
27468 TAATAAGCAC
27478 TAATGATAA
1 TAATGATAA
*
27487 TAATAATAA
1 TAATGATAA
*
27496 TAATAATAA
1 TAATGATAA
* *
27505 TAATAATGA
1 TAATGATAA
* *
27514 TGATGATGA
1 TAATGATAA
*
27523 TGATGATAA
1 TAATGATAA
*
27532 TGATGATAA
1 TAATGATAA
27541 CAGAACGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.33
Consensus pattern (9 bp):
TAATGATAA
Found at i:32349 original size:21 final size:21
Alignment explanation
Indices: 32323--32379 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
32313 GTGCCTAGTA
*
32323 GGCTTTGTGCCGGTGTAATCG
1 GGCTTTGTGCCAGTGTAATCG
*
32344 GGCTTTGTGCCAGTGTAATTG
1 GGCTTTGTGCCAGTGTAATCG
* *
32365 AGTTTTGTGCCAGTG
1 GGCTTTGTGCCAGTG
32380 ACCAAAGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.12, C:0.16, G:0.35, T:0.37
Consensus pattern (21 bp):
GGCTTTGTGCCAGTGTAATCG
Done.