Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015347.1 Kokia drynarioides strain JFW-HI SEQ_130394, 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: 410906
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 895 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:371914 original size:7 final size:7
Alignment explanation
Indices: 371902--371939 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
371892 GGGAAGCCAA
*
371902 GGCCAGT
1 GGCCAGC
371909 GGCCAGC
1 GGCCAGC
371916 GGCCAGC
1 GGCCAGC
371923 GGCCAGC
1 GGCCAGC
371930 GGCCAGC
1 GGCCAGC
371937 GGC
1 GGC
371940 ATGTTTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.13, C:0.39, G:0.45, T:0.03
Consensus pattern (7 bp):
GGCCAGC
Found at i:377093 original size:24 final size:24
Alignment explanation
Indices: 377071--377117 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
377061 GAAAGAAATA
* * *
377071 ATAAAA-ATTTTATATTAGTAAAT
1 ATAAAATATATTATACTAATAAAT
377094 ATAAAATATATTATACTAATAAAT
1 ATAAAATATATTATACTAATAAAT
377118 GTTAAATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
ATAAAATATATTATACTAATAAAT
Found at i:378069 original size:28 final size:28
Alignment explanation
Indices: 378038--378099 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
378028 AAATGAGACT
*
378038 TTTTGGATACCCGGGGGAAAAATGGTAA
1 TTTTGGATACCCGAGGGAAAAATGGTAA
* * *
378066 TTTTGGATTCTCGAGGGCAAAATGGTAA
1 TTTTGGATACCCGAGGGAAAAATGGTAA
378094 TTTTGG
1 TTTTGG
378100 GAAAATACGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.31, T:0.32
Consensus pattern (28 bp):
TTTTGGATACCCGAGGGAAAAATGGTAA
Found at i:378170 original size:29 final size:28
Alignment explanation
Indices: 378138--378264 Score: 73
Period size: 30 Copynumber: 4.4 Consensus size: 28
378128 TAGACATTCA
378138 GAGGGTAAAAGGGTAATTTTGAGAGTTTT
1 GAGGGTAAAAGGGTAATTTTG-GAGTTTT
**
378167 GA-GGTCAAAAATGGAGT--TTTTGGACATTT
1 GAGGGT--AAAA-GG-GTAATTTTGGAGTTTT
* * *
378196 GGGGGTAAAATGGTAATTTTTGAAAGTTTT
1 GAGGGTAAAAGGGTAA-TTTTG-GAGTTTT
* * *
378226 G-GGGTTAAAAATGGAAATTTTGGAGGTTT
1 GAGGG-T-AAAAGGGTAATTTTGGAGTTTT
378255 GAGGGTAAAA
1 GAGGGTAAAA
378265 ATGGAATTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 25
0.68 0.09 0.23
Matches are distributed among these distances:
26 2 0.03
27 1 0.01
28 11 0.14
29 23 0.30
30 26 0.34
31 11 0.14
32 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.34
Consensus pattern (28 bp):
GAGGGTAAAAGGGTAATTTTGGAGTTTT
Found at i:378179 original size:59 final size:59
Alignment explanation
Indices: 378114--378299 Score: 166
Period size: 59 Copynumber: 3.2 Consensus size: 59
378104 ATACGGGGTT
*
378114 AAAAATGGAATATTTAGACATTCAGAGGGTAAAAGGGTAA-TTTTGAGAGTTTTGAGGTC
1 AAAAATGGAATATTTAGACATT-AGAGGGTAAAAGGGTAATTTTTGAAAGTTTTGAGGTC
* * * * * * * *
378173 AAAAATGGAGTTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTT
1 AAAAATGGAATATTTAGACATTAGAGGGTAAAAGGGTAATTTTTGAAAGTTTTGAGGTC
* ** * * * *
378232 AAAAATGGAA-ATTTTGGAGGTTTGAGGGTAAAAATGG-AATTTTTGGAA--TTTGGGGTC
1 AAAAATGGAATA-TTTAGACATTAGAGGGT-AAAAGGGTAATTTTTGAAAGTTTTGAGGTC
378289 AAAAATGGAAT
1 AAAAATGGAAT
378300 TTTTGGAAGT
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
57 18 0.17
58 14 0.13
59 68 0.64
60 7 0.07
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAAATGGAATATTTAGACATTAGAGGGTAAAAGGGTAATTTTTGAAAGTTTTGAGGTC
Found at i:378205 original size:88 final size:87
Alignment explanation
Indices: 378108--378362 Score: 236
Period size: 87 Copynumber: 2.9 Consensus size: 87
378098 GGGAAAATAC
* * * *
378108 GGGGTTAAAAATGGAATATTTAGACA-TTCAGAGGG-T-AAAAGGGTAATTTTGAGAGTTTTGA-
1 GGGGGTAAAAATGGAAT-TTTAGAAAGTTCAG-GGGTTAAAAAGGGAAATTTTG-GAGGTTTGAG
*
378169 GGTCAAAAATGGAGTTTTTGGACATTT
63 GGT-AAAAATGGAATTTTTGGA-ATTT
* ** *
378196 GGGGGT-AAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATGGAAATTTTGGAGGTTTGAGGG
1 GGGGGTAAAAATGG-AATTTTAGAAAGTTCAGGGGTTAAAAAGGGAAATTTTGGAGGTTTGAGGG
378260 TAAAAATGGAATTTTTGGAATTT
65 TAAAAATGGAATTTTTGGAATTT
* * ** * * * *
378283 -GGGGTCAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGG-AATTTTGGAAGTTTGGGGG
1 GGGGGT-AAAAATGGAATTTTAGAAAGTTCAGGGGTTAAAAAGGGAAATTTTGGAGGTTTGAGGG
*
378346 TAAAAATGTAATTTTTG
65 TAAAAATGGAATTTTTG
378363 AACAGTTTAG
Statistics
Matches: 146, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
86 38 0.26
87 48 0.33
88 44 0.30
89 16 0.11
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (87 bp):
GGGGGTAAAAATGGAATTTTAGAAAGTTCAGGGGTTAAAAAGGGAAATTTTGGAGGTTTGAGGGT
AAAAATGGAATTTTTGGAATTT
Found at i:378229 original size:30 final size:30
Alignment explanation
Indices: 378173--378362 Score: 211
Period size: 29 Copynumber: 6.5 Consensus size: 30
378163 TTTTGAGGTC
*
378173 AAAAATGGAGTTTTTGGACA--TTTGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTTGGGGGT
* *
378202 -AAAATGGTAATTTTTGAAAGTTTTGGGGTT
1 AAAAATGG-AATTTTTGGAAGTTTTGGGGGT
* * *
378232 AAAAATGGAAATTTTGG-AGGTTTGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGGT
378261 AAAAATGGAATTTTTGGAA--TTT-GGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGGT
378288 CAAAAATGGAATTTTTGGAAGTTTT-GGGGT
1 -AAAAATGGAATTTTTGGAAGTTTTGGGGGT
378318 CAAAAATGGAA-TTTTGGAAG-TTTGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTTGGGGGT
*
378347 AAAAATGTAATTTTTG
1 AAAAATGGAATTTTTG
378363 AACAGTTTAG
Statistics
Matches: 140, Mismatches: 11, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.03
28 42 0.30
29 52 0.37
30 35 0.25
31 7 0.05
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTTGGGGGT
Found at i:379415 original size:3 final size:3
Alignment explanation
Indices: 379402--379469 Score: 109
Period size: 3 Copynumber: 22.3 Consensus size: 3
379392 TTCCTTTTTA
* *
379402 ATT AAT ATT ATT ATT AAT ATT ATTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
379448 ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
379470 ATGCTATTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:379508 original size:4 final size:4
Alignment explanation
Indices: 379501--379532 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
379491 TATATATATA
379501 TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
379533 ACACTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:379772 original size:61 final size:61
Alignment explanation
Indices: 379677--379802 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
379667 GTTCGAATCT
379677 ATTGGATATTGATAAAAGAACAAAATGTGTATGGATTGCTAAAAGGCTTGAGTTAAATTCG
1 ATTGGATATTGATAAAAGAACAAAATGTGTATGGATTGCTAAAAGGCTTGAGTTAAATTCG
379738 ATTGGATATTGATAAAAGAACAAAATGTGTATGGATTGCTAAAAGGCTTGAGTTAAATTCG
1 ATTGGATATTGATAAAAGAACAAAATGTGTATGGATTGCTAAAAGGCTTGAGTTAAATTCG
379799 ATTG
1 ATTG
379803 TTTTTTCAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (61 bp):
ATTGGATATTGATAAAAGAACAAAATGTGTATGGATTGCTAAAAGGCTTGAGTTAAATTCG
Found at i:381796 original size:31 final size:31
Alignment explanation
Indices: 381761--381833 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
381751 TTTAGTTTAT
381761 AATTCGATACTTAAGTATGGTTTCAATGTTC
1 AATTCGATACTTAAGTATGGTTTCAATGTTC
381792 AATTCGATACTTAAGTATGGTTTCAATGTTC
1 AATTCGATACTTAAGTATGGTTTCAATGTTC
381823 AATTCGATACT
1 AATTCGATACT
381834 CAAACTAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (31 bp):
AATTCGATACTTAAGTATGGTTTCAATGTTC
Found at i:386361 original size:23 final size:23
Alignment explanation
Indices: 386331--386434 Score: 110
Period size: 23 Copynumber: 4.6 Consensus size: 23
386321 GAAACAATAA
386331 GCACACACAGTGC-AATCTAGTAG
1 GCACACACAGTGCAAATC-AGTAG
386354 GCACACACAGTGC-AATCAGTAG
1 GCACACACAGTGCAAATCAGTAG
*
386376 GCACACATCA-CGCAAATCAGTAG
1 GCACACA-CAGTGCAAATCAGTAG
* *
386399 GCACACGA-GGTGCGAAA-CAGTAA
1 GCACAC-ACAGTGC-AAATCAGTAG
386422 GCACACACAGTGC
1 GCACACACAGTGC
386435 TGAACGGTAA
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
22 15 0.21
23 51 0.73
24 4 0.06
ACGTcount: A:0.37, C:0.28, G:0.23, T:0.12
Consensus pattern (23 bp):
GCACACACAGTGCAAATCAGTAG
Found at i:386382 original size:45 final size:46
Alignment explanation
Indices: 386321--386434 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 46
386311 AAGTGCTAGG
*
386321 GAAACAATAAGCACACACAGTGC-AATCTAGTAGGCACAC-ACAGTGC
1 GAAACAGTAAGCACACACAGTGCAAATC-AGTAGGCACACGA-AGTGC
* * * *
386367 -AATCAGTAGGCACACATCA-CGCAAATCAGTAGGCACACGAGGTGC
1 GAAACAGTAAGCACACA-CAGTGCAAATCAGTAGGCACACGAAGTGC
386412 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAAGCACACACAGTGC
386435 TGAACGGTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
45 32 0.58
46 23 0.42
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.12
Consensus pattern (46 bp):
GAAACAGTAAGCACACACAGTGCAAATCAGTAGGCACACGAAGTGC
Found at i:389519 original size:31 final size:31
Alignment explanation
Indices: 389484--389556 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
389474 TTTAGTTTAT
389484 AATTCGATACTTAAGTATGGTTTCAATGTTC
1 AATTCGATACTTAAGTATGGTTTCAATGTTC
389515 AATTCGATACTTAAGTATGGTTTCAATGTTC
1 AATTCGATACTTAAGTATGGTTTCAATGTTC
389546 AATTCGATACT
1 AATTCGATACT
389557 CAAACTAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (31 bp):
AATTCGATACTTAAGTATGGTTTCAATGTTC
Found at i:394084 original size:23 final size:23
Alignment explanation
Indices: 394054--394157 Score: 110
Period size: 23 Copynumber: 4.6 Consensus size: 23
394044 GAAACAATAA
394054 GCACACACAGTGC-AATCTAGTAG
1 GCACACACAGTGCAAATC-AGTAG
394077 GCACACACAGTGC-AATCAGTAG
1 GCACACACAGTGCAAATCAGTAG
*
394099 GCACACATCA-CGCAAATCAGTAG
1 GCACACA-CAGTGCAAATCAGTAG
* *
394122 GCACACGA-GGTGCGAAA-CAGTAA
1 GCACAC-ACAGTGC-AAATCAGTAG
394145 GCACACACAGTGC
1 GCACACACAGTGC
394158 TGAACGGTAA
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
22 15 0.21
23 51 0.73
24 4 0.06
ACGTcount: A:0.37, C:0.28, G:0.23, T:0.12
Consensus pattern (23 bp):
GCACACACAGTGCAAATCAGTAG
Found at i:394105 original size:45 final size:46
Alignment explanation
Indices: 394044--394157 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 46
394034 AAGTGCTAGG
*
394044 GAAACAATAAGCACACACAGTGC-AATCTAGTAGGCACAC-ACAGTGC
1 GAAACAGTAAGCACACACAGTGCAAATC-AGTAGGCACACGA-AGTGC
* * * *
394090 -AATCAGTAGGCACACATCA-CGCAAATCAGTAGGCACACGAGGTGC
1 GAAACAGTAAGCACACA-CAGTGCAAATCAGTAGGCACACGAAGTGC
394135 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAAGCACACACAGTGC
394158 TGAACGGTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
45 32 0.58
46 23 0.42
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.12
Consensus pattern (46 bp):
GAAACAGTAAGCACACACAGTGCAAATCAGTAGGCACACGAAGTGC
Found at i:399572 original size:16 final size:17
Alignment explanation
Indices: 399537--399568 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
399527 TAAGATGAGA
399537 AGAAGAAGAAGAAAATG
1 AGAAGAAGAAGAAAATG
399554 AGAA-AAGAA-AAAATG
1 AGAAGAAGAAGAAAATG
399569 GAGATGCCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (17 bp):
AGAAGAAGAAGAAAATG
Found at i:401054 original size:7 final size:7
Alignment explanation
Indices: 401044--401069 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
401034 CTCAAACCTC
401044 ATCCATT
1 ATCCATT
401051 ATCCATT
1 ATCCATT
401058 ATCCATT
1 ATCCATT
401065 ATCCA
1 ATCCA
401070 AAGTTGGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (7 bp):
ATCCATT
Found at i:407368 original size:16 final size:16
Alignment explanation
Indices: 407324--407375 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
407314 CTTAAAATAG
407324 TAAAATTTT-AATTTA
1 TAAAATTTTAAATTTA
**
407339 T-ATTTTTTATAATTTA
1 TAAAATTTTA-AATTTA
*
407355 TAAAATTTTAAATTGA
1 TAAAATTTTAAATTTA
407371 TAAAA
1 TAAAA
407376 ATATATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 5 0.17
15 1 0.03
16 17 0.59
17 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Done.