Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002765.1 Kokia drynarioides strain JFW-HI SEQ_115087, 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: 13248
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:3172 original size:30 final size:30
Alignment explanation
Indices: 3137--3322 Score: 155
Period size: 30 Copynumber: 6.2 Consensus size: 30
3127 TGTTTATTTT
* * *
3137 AAAATTATATTTTTACCCCCGAACTTTCCA
1 AAAATTATAATTTAACCCCTGAACTTTCCA
* * * *
3167 AAAATTAAAAATTT-ACACCTAAACTTTCTA
1 AAAATT-ATAATTTAACCCCTGAACTTTCCA
*
3197 AAAATT-TGAATTTAACCCCTAAACTTTCCA
1 AAAATTAT-AATTTAACCCCTGAACTTTCCA
*
3227 AAAATTCA-AATTTAACGCCTGAACTTTCCA
1 AAAATT-ATAATTTAACCCCTGAACTTTCCA
** * * * *
3257 AATTTTAGAATTTTACCCC-CAAGCTTTCAA
1 AAAATTATAATTTAACCCCTGAA-CTTTCCA
* *
3287 AAAATTATAATTTAACCCTTGAACTTTCAA
1 AAAATTATAATTTAACCCCTGAACTTTCCA
3317 AAAATT
1 AAAATT
3323 TGAATTTGCC
Statistics
Matches: 125, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
29 8 0.06
30 110 0.88
31 7 0.06
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTATAATTTAACCCCTGAACTTTCCA
Found at i:3230 original size:60 final size:58
Alignment explanation
Indices: 3151--3329 Score: 189
Period size: 60 Copynumber: 3.0 Consensus size: 58
3141 TTATATTTTT
* *
3151 ACCCCCGAACTTTCCAAAAATTAAAAATTTACACCTAAACTTTCTAAAAATTTGAATTTA
1 ACCCCCAAACTTTCCAAAAATT-AAAATTTACACCTGAACTTTC-AAAAATTTGAATTTA
* * * * * *
3211 ACCCCTAAACTTTCCAAAAATTCAAATTTAACGCCTGAACTTTCCAAATTTTAGAATTTT
1 ACCCCCAAACTTTCCAAAAATTAAAATTT-ACACCTGAACTTTCAAAAATTT-GAATTTA
* * *
3271 ACCCCCAAGCTTTCAAAAAATTATAATTTA-ACCCTTGAACTTTCAAAAAATTTGAATTT
1 ACCCCCAAACTTTCCAAAAATTAAAATTTACA-CC-TGAACTTTC-AAAAATTTGAATTT
3330 GCCCCGATTT
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
59 15 0.15
60 77 0.79
61 6 0.06
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (58 bp):
ACCCCCAAACTTTCCAAAAATTAAAATTTACACCTGAACTTTCAAAAATTTGAATTTA
Found at i:3329 original size:90 final size:90
Alignment explanation
Indices: 3157--3322 Score: 217
Period size: 90 Copynumber: 1.8 Consensus size: 90
3147 TTTTACCCCC
* *
3157 GAACTTTCCAAAAATTAAAAATTTACACCTAAACTTTCTAAAAATTTGAATTTAACCCCTAAACT
1 GAACTTTCCAAAAATTAAAAATTTACACCCAAACTTTCAAAAAATTTGAATTTAACCCCTAAACT
*
3222 TTCCAAAAATTCAAATTTAACGCCT
66 TTCAAAAAATTCAAATTTAACGCCT
** * * * * * *
3247 GAACTTTCCAAATTTTAGAATTTTACCCCCAAGCTTTCAAAAAATTAT-AATTTAACCCTTGAAC
1 GAACTTTCCAAAAATTAAAAATTTACACCCAAACTTTCAAAAAATT-TGAATTTAACCCCTAAAC
3311 TTTCAAAAAATT
65 TTTCAAAAAATT
3323 TGAATTTGCC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
90 63 0.98
91 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (90 bp):
GAACTTTCCAAAAATTAAAAATTTACACCCAAACTTTCAAAAAATTTGAATTTAACCCCTAAACT
TTCAAAAAATTCAAATTTAACGCCT
Found at i:3473 original size:19 final size:20
Alignment explanation
Indices: 3449--3495 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3439 TGTATATTAT
* *
3449 TTTATTTGTTTGTTC-TTTA
1 TTTATTTATTTGTTCAGTTA
*
3468 TTTATTCATTTGTTCAGTTA
1 TTTATTTATTTGTTCAGTTA
3488 TTTATTTA
1 TTTATTTA
3496 CTTAATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.17, C:0.06, G:0.09, T:0.68
Consensus pattern (20 bp):
TTTATTTATTTGTTCAGTTA
Found at i:4634 original size:25 final size:25
Alignment explanation
Indices: 4606--4678 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
4596 CTTCTAGTAA
4606 TTTAGCTCATACGAGCCTAGACAAC
1 TTTAGCTCATACGAGCCTAGACAAC
* **
4631 TTTAGCTCACACGAGCCTAGA-ATG
1 TTTAGCTCATACGAGCCTAGACAAC
* * *
4655 GTTAGCTCTTGCGAGCCTAGACAA
1 TTTAGCTCATACGAGCCTAGACAA
4679 AGTTTAACCA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 18 0.46
25 21 0.54
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (25 bp):
TTTAGCTCATACGAGCCTAGACAAC
Found at i:4849 original size:82 final size:82
Alignment explanation
Indices: 4694--4914 Score: 352
Period size: 82 Copynumber: 2.7 Consensus size: 82
4684 AACCAGTATA
* * * * * *
4694 CGATGCTGCTTACACAAGCTGATGAGAATCCGTGACATATGTGAAGACTCAGCCATCGATACGGT
1 CGATGCTGCTCACACAAGCTGATGAGAATCCGCGACATACGAGAAGACTCAGCCATCAATACGAT
4759 CCAAAATTTTCCACTCT
66 CCAAAATTTTCCACTCT
* *
4776 CGATACTGCTCACACAAGCTGATGAGAATCCGCGACATACGAGAAGACTCAGCCATCAATATGAT
1 CGATGCTGCTCACACAAGCTGATGAGAATCCGCGACATACGAGAAGACTCAGCCATCAATACGAT
*
4841 CCAGAATTTTCCACTCT
66 CCAAAATTTTCCACTCT
*
4858 CGATGCTGCTCACACAAGCTGATGAGAATCCGCGACATACGCGAAGACTCAGCCATC
1 CGATGCTGCTCACACAAGCTGATGAGAATCCGCGACATACGAGAAGACTCAGCCATC
4915 GTAGGGATCT
Statistics
Matches: 128, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 128 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (82 bp):
CGATGCTGCTCACACAAGCTGATGAGAATCCGCGACATACGAGAAGACTCAGCCATCAATACGAT
CCAAAATTTTCCACTCT
Found at i:8369 original size:16 final size:17
Alignment explanation
Indices: 8350--8431 Score: 66
Period size: 16 Copynumber: 4.8 Consensus size: 17
8340 AAAAATAAAA
8350 ATTTAATTTAATA-ATT
1 ATTTAATTTAATATATT
*
8366 ATTTTAA--TAAAATATT
1 A-TTTAATTTAATATATT
*
8382 A-TTAATTTAATATAAT
1 ATTTAATTTAATATATT
8398 ATTT-ATCTTAATAAATATT
1 ATTTAAT-TTAAT--ATATT
8417 ATATTAATTTAATAT
1 AT-TTAATTTAATAT
8432 TAAAGTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
14 4 0.08
15 4 0.08
16 15 0.29
17 12 0.23
18 2 0.04
19 6 0.12
20 7 0.13
21 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAATTTAATATATT
Found at i:8414 original size:21 final size:20
Alignment explanation
Indices: 8358--8430 Score: 57
Period size: 21 Copynumber: 3.8 Consensus size: 20
8348 AAATTTAATT
*
8358 TAATAATTATTTTAATAAA-A
1 TAAT-ATTAATTTAATAAATA
*
8378 TATTATTAA-TT--T-AATA
1 TAATATTAATTTAATAAATA
*
8394 TAATATTTATCTTAATAAATA
1 TAATATTAAT-TTAATAAATA
*
8415 TTATATTAATTTAATA
1 TAATATTAATTTAATA
8431 TTAAAGTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
15 2 0.05
16 9 0.22
18 4 0.10
19 4 0.10
20 10 0.24
21 12 0.29
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATATTAATTTAATAAATA
Done.