Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001942.1 Kokia drynarioides strain JFW-HI SEQ_113764, 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: 70115
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:21728 original size:19 final size:21
Alignment explanation
Indices: 21698--21738 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
21688 TCTTTTCTAA
*
21698 TCTTTATTTGTT-ACTAGTTT
1 TCTTTATTTGTTGACTACTTT
21718 TCTTT-TTTGTTGACTACTTT
1 TCTTTATTTGTTGACTACTTT
21738 T
1 T
21739 ACATTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.66
Consensus pattern (21 bp):
TCTTTATTTGTTGACTACTTT
Found at i:34958 original size:21 final size:21
Alignment explanation
Indices: 34920--34959 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34910 TCTAATCTTT
*
34920 TTTAGGTTTTAAGTTTAGTAG
1 TTTAGGTTTTAAGCTTAGTAG
34941 TTTAGGATTTTAA-CTTAGT
1 TTTAGG-TTTTAAGCTTAGT
34960 TTTATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.25, C:0.03, G:0.20, T:0.53
Consensus pattern (21 bp):
TTTAGGTTTTAAGCTTAGTAG
Found at i:37249 original size:17 final size:17
Alignment explanation
Indices: 37211--37249 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
37201 TTGAAGTTTA
37211 TTATTCTTGTAAATATT
1 TTATTCTTGTAAATATT
* * *
37228 GTATTCTTGTATATTTT
1 TTATTCTTGTAAATATT
37245 TTATT
1 TTATT
37250 TGAGGAGCTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (17 bp):
TTATTCTTGTAAATATT
Found at i:39841 original size:195 final size:194
Alignment explanation
Indices: 39413--39858 Score: 517
Period size: 194 Copynumber: 2.3 Consensus size: 194
39403 TACCAGTACC
* * * * *
39413 CGATGCTACTCACACGAGCTGTCGAGAACTTGCAACATATGCGGTACCCCAGCCATC-AGTACAG
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGTCATCGAGTACAG
* * *
39477 TGTCTGTCTGTAAACTGTCCCCTAAAGATGCTACTCACACGAGCTGTCGAGAATATGCATTCAAG
66 TATCTGTCTATAAACTGTCCCCTAAAGATGCTACTCACACGAACTGTCGAGAATATGCATTCAAG
* * * * * ***
39542 CATAAATCCCAGCCATCGTAGGGCCTATAGTCCATTTTGGATTTCATATTTCTTTTCTGTCTCA
131 CATAAATCCCAGCCACCATAAGGCCTATAATCCATTTTGGATTTCATATTTCTTTCCCAACTCA
* * * **
39606 CGATGTTTCTCACACGAGCTGTCGAGGACTCGTAACATATGTGGTACCTCAGTCATCGA-TATGG
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGTCATCGAGTACAG
* * * *
39670 TATCTGTGC-ATATAATTGTTCCCTAATGATGCTGCTCACACGAACTGTCGAGAATATGCACTT-
66 TATCTGT-CTATA-AACTGTCCCCTAAAGATGCTACTCACACGAACTGTCGAGAATATGCA-TTC
* * *
39733 ATGCATAAATCTCAGCCACCATAAGGCCTGTAATCCATTCTTGGA-TTCAT-TTCTCATTTCCCA
128 AAGCATAAATCCCAGCCACCATAAGGCCTATAATCCATT-TTGGATTTCATATT-TC-TTTCCCA
39796 ACTCA
190 ACTCA
* * *
39801 CGATGCTACTTACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAATCATCG
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGTCATCG
39859 TGTCGGTTTC
Statistics
Matches: 212, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
193 62 0.29
194 83 0.39
195 67 0.32
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (194 bp):
CGATGCTACTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGTCATCGAGTACAG
TATCTGTCTATAAACTGTCCCCTAAAGATGCTACTCACACGAACTGTCGAGAATATGCATTCAAG
CATAAATCCCAGCCACCATAAGGCCTATAATCCATTTTGGATTTCATATTTCTTTCCCAACTCA
Found at i:41403 original size:20 final size:20
Alignment explanation
Indices: 41373--41456 Score: 105
Period size: 20 Copynumber: 4.2 Consensus size: 20
41363 TTCAGAAAAA
* *
41373 GTCAATGATCAAAGTCAACG
1 GTCAACGATCAAAGTCAATG
* *
41393 ATCAACTATCAAAGTCAATG
1 GTCAACGATCAAAGTCAATG
*
41413 GTCAACGGTCAAAGTCAATG
1 GTCAACGATCAAAGTCAATG
*
41433 GTCAACGATCAACGGTCAATG
1 GTCAACGATCAA-AGTCAATG
41454 GTC
1 GTC
41457 GATCAATGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 44 0.81
21 10 0.19
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
GTCAACGATCAAAGTCAATG
Found at i:41456 original size:7 final size:7
Alignment explanation
Indices: 41406--41456 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
41396 AACTATCAAA
*
41406 GTCAATG
1 GTCAACG
41413 GTCAACG
1 GTCAACG
*
41420 GTCAA-A
1 GTCAACG
*
41426 GTCAATG
1 GTCAACG
41433 GTCAACG
1 GTCAACG
*
41440 ATCAACG
1 GTCAACG
*
41447 GTCAATG
1 GTCAACG
41454 GTC
1 GTC
41457 GATCAATGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (7 bp):
GTCAACG
Found at i:41464 original size:11 final size:11
Alignment explanation
Indices: 41448--41499 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
41438 CGATCAACGG
41448 TCAATGGTCGA
1 TCAATGGTCGA
*
41459 TCAATGGTCGG
1 TCAATGGTCGA
* *
41470 TCAACGATC-A
1 TCAATGGTCGA
*
41480 GTCAACGGTCGA
1 -TCAATGGTCGA
41492 TCAATGGT
1 TCAATGGT
41500 TTGACTTGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 32 0.97
12 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (11 bp):
TCAATGGTCGA
Found at i:41473 original size:22 final size:22
Alignment explanation
Indices: 41445--41499 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
41435 CAACGATCAA
*
41445 CGGTCAATGGTC-GATCAATGGT
1 CGGTCAATGGTCAG-TCAACGGT
* *
41467 CGGTCAACGATCAGTCAACGGT
1 CGGTCAATGGTCAGTCAACGGT
*
41489 CGATCAATGGT
1 CGGTCAATGGT
41500 TTGACTTGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (22 bp):
CGGTCAATGGTCAGTCAACGGT
Found at i:45523 original size:20 final size:20
Alignment explanation
Indices: 45482--45524 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
45472 TTTAACGTTA
* *
45482 ATTAAAAATATTTTCATGTT
1 ATTAAAAATATTTTAATATT
45502 ATTAAAAAT-TTATTAATATT
1 ATTAAAAATATT-TTAATATT
45522 ATT
1 ATT
45525 GAAATTGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTAAAAATATTTTAATATT
Found at i:66426 original size:2 final size:2
Alignment explanation
Indices: 66392--66417 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
66382 CCTCAGTCGA
66392 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
66418 GTTTATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.