Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012923.1 Kokia drynarioides strain JFW-HI SEQ_127939, 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: 8458
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Found at i:2783 original size:95 final size:96
Alignment explanation
Indices: 2606--2785 Score: 231
Period size: 95 Copynumber: 1.9 Consensus size: 96
2596 AGGACGTTCG
* * * *
2606 ATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGGT
1 ATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTGAAGGCGCAAATTTTCAAAATCGAAGAT
* *
2671 AAGGAAACATTGTCTCGATTAAGGGTATTCA
66 AAAGAAACATTGCCTCGATTAAGGGTATTCA
* * *
2702 ATTATTTCGATTTGTAGAAA-ATTGCACCTAGTAAGTGAAGGCGTAAATTTTCAAAACTCGAA-A
1 ATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTGAAGGCGCAAATTTTCAAAA-TCGAAGA
*
2765 TAAA-AGAATATTGCCTCGATT
65 TAAAGA-AACATTGCCTCGATT
2786 TTAAAGTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
94 1 0.01
95 48 0.67
96 23 0.32
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTGAAGGCGCAAATTTTCAAAATCGAAGAT
AAAGAAACATTGCCTCGATTAAGGGTATTCA
Found at i:3193 original size:30 final size:30
Alignment explanation
Indices: 3015--3209 Score: 95
Period size: 30 Copynumber: 6.6 Consensus size: 30
3005 AGATACCCTA
*
3015 GGGGCAAAATGGTAA-TTTTG-GATTTTCG
1 GGGGCAAAATGGTAATTTTTGAAATTTTCG
* * *
3043 AGGGCAAAATGGTAATTTTGGGAAAGTTTT-A
1 GGGGCAAAATGGTAATTTT-TGAAA-TTTTCG
*** *
3074 GGTTAAAAATGG-AATTTTTTAGACATTTT--
1 GGGGCAAAATGGTAA-TTTTT-GAAATTTTCG
* * * * *
3103 GGGGTAAAAGGGTAA-TTTTGAGAGTTTCC
1 GGGGCAAAATGGTAATTTTTGAAATTTTCG
* * * *
3132 AGGTCGAAAATGG-AGTTTTTGGACA--TTCG
1 GGGGC-AAAATGGTAATTTTT-GAAATTTTCG
3161 GGGGCAAAATGGTAATTTTTGAAATTTTCG
1 GGGGCAAAATGGTAATTTTTGAAATTTTCG
* *
3191 GGGTCAAAATGGAAATTTT
1 GGGGCAAAATGGTAATTTT
3210 GGAGGTTCAA
Statistics
Matches: 123, Mismatches: 29, Indels: 28
0.68 0.16 0.16
Matches are distributed among these distances:
27 6 0.05
28 28 0.23
29 26 0.21
30 40 0.33
31 19 0.15
32 4 0.03
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (30 bp):
GGGGCAAAATGGTAATTTTTGAAATTTTCG
Found at i:3210 original size:58 final size:58
Alignment explanation
Indices: 3015--3212 Score: 159
Period size: 58 Copynumber: 3.4 Consensus size: 58
3005 AGATACCCTA
* ** * *
3015 GGGG-CAAAATGGTAATTTTGGATTTTCGAGGGCAAAATGGTAATTTTGGGAAAGTTTT-
1 GGGGTCAAAATGGAAATTTTGGACATTCGGGGGCAAAATGGTAATTTT-TGAAA-TTTTC
* * * * * ** * * * *
3073 AGGTTAAAAATGGAATTTTTTAGACATTTTGGGGTAAAAGGGTAA-TTTTGAGAGTTTC
1 GGGGTCAAAATGGAA-ATTTTGGACATTCGGGGGCAAAATGGTAATTTTTGAAATTTTC
** **
3131 CAGGTCGAAAATGGAGTTTTTGGACATTCGGGGGCAAAATGGTAATTTTTGAAATTTTC
1 GGGGTC-AAAATGGAAATTTTGGACATTCGGGGGCAAAATGGTAATTTTTGAAATTTTC
3190 GGGGTCAAAATGGAAATTTTGGA
1 GGGGTCAAAATGGAAATTTTGGA
3213 GGTTCAAGGG
Statistics
Matches: 103, Mismatches: 32, Indels: 10
0.71 0.22 0.07
Matches are distributed among these distances:
57 3 0.03
58 46 0.45
59 34 0.33
60 20 0.19
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (58 bp):
GGGGTCAAAATGGAAATTTTGGACATTCGGGGGCAAAATGGTAATTTTTGAAATTTTC
Found at i:3246 original size:50 final size:51
Alignment explanation
Indices: 3181--3280 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
3171 GGTAATTTTT
* *
3181 GAAATTTTCGGGGTC-AAAATGGAAATTTTGGAGGTTCAAGGGTAAAAATG
1 GAAAGTTTCGGGGTCAAAAATGGAAATTTTGGAAGTTCAAGGGTAAAAATG
* *
3231 GAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAT
1 GAAAGTTTCGGGGTCAAAAATGGAAATTTTGGAAGTTCAAGGGTAAAAAT
3281 AGAATTTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 14 0.31
51 31 0.69
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (51 bp):
GAAAGTTTCGGGGTCAAAAATGGAAATTTTGGAAGTTCAAGGGTAAAAATG
Found at i:3278 original size:29 final size:29
Alignment explanation
Indices: 3237--3292 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
3227 AATGGAAAGT
*
3237 TTCGGGGTCAAAAATGGAATTTTTGGAAG
1 TTCGGGGTCAAAAATAGAATTTTTGGAAG
3266 TTCGAGGGT-AAAAATAGAATTTTTGGA
1 TTCG-GGGTCAAAAATAGAATTTTTGGA
3293 TGTATTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (29 bp):
TTCGGGGTCAAAAATAGAATTTTTGGAAG
Found at i:7202 original size:115 final size:114
Alignment explanation
Indices: 7053--7377 Score: 384
Period size: 116 Copynumber: 2.8 Consensus size: 114
7043 TTAAACCTAT
* * * * *
7053 GCTCGATGTGAGCAAATCCTCGAACCCCAACTTCCTGATAAGATACTGAGAAGTAGGTCGAAATA
1 GCTCGATGTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAG-AGGTCGAAACA
* * *
7118 ATGAAATGGTTAGCTTCCTGATGAGACT-CAGAGGAGTATACCAACTCAGG
65 ATGAAATGGTTAGCTTCCTGATGAGA-TACAAAGAAGAATACCAACTCAGG
* * * * *
7168 GCTCGATGTGATCAAATCTTCAAATCCCAGCTTCCTGATGAGATACAGAGAAGCGGATTGAAACA
1 GCTCGATGTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGAGG-TCGAAACA
** * * *
7233 A-GTAAGGCGGTCATCTTCCTGATGAGATACAAAGAAGAATATCAACTCAGG
65 ATG-AA-ATGGTTAGCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGG
* * *
7284 ACTCGATGCGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAG-AGGTCGAAACA
*
7349 ATAAAATGGTTAGCTTCCTGATGAGATAC
65 ATGAAATGGTTAGCTTCCTGATGAGATAC
7378 TGAGAAGTGA
Statistics
Matches: 173, Mismatches: 31, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
114 3 0.02
115 76 0.44
116 92 0.53
117 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (114 bp):
GCTCGATGTGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGAGGTCGAAACAA
TGAAATGGTTAGCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGG
Found at i:7300 original size:116 final size:114
Alignment explanation
Indices: 6962--7337 Score: 364
Period size: 116 Copynumber: 3.2 Consensus size: 114
6952 CCAAATTCGT
* * *
6962 CTTCCTGATGAGATACAGAGAAACGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAG-TAAGCGGTCATCTTCCTGATGAGATAC
* * * * * *
7027 TGAGAAGAAGACCAAATTAAAC-CTATGCTCGATGTGAGCAAATCCTCGAACCCCAA
65 --A-AAGAAGA--ATA-TCAACTC-AGGCTCGATGTGAGCAAATCTTCAAACCCCAG
* * * * * ** * *
7083 CTTCCTGATAAGATACTGAGAAGTAGG-TCGAAATAA-TGAAATGGTTAGCTTCCTGATGAGACT
1 CTTCCTGATGAGATACAGAGAAG-CGGATTGAAACAAGT-AAGCGGTCATCTTCCTGATGAGA-T
* * * * * *
7146 -CAGAGGAGTATACCAACTCAGGGCTCGATGTGATCAAATCTTCAAATCCCAG
63 ACAAAGAAGAATATCAACTCA-GGCTCGATGTGAGCAAATCTTCAAACCCCAG
7198 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTAAGGCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTAA-GCGGTCATCTTCCTGATGAGATAC
*
7263 AAAGAAGAATATCAACTCAGGACTCGATGCGAGCAAATCTTCAAACCCCAG
65 AAAGAAGAATATCAACTCAGG-CTCGATGTGAGCAAATCTTCAAACCCCAG
*
7314 CTTCCTGATGAGATACTGAGAAGC
1 CTTCCTGATGAGATACAGAGAAGC
7338 AGGTCGAAGC
Statistics
Matches: 204, Mismatches: 41, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
114 6 0.03
115 61 0.30
116 83 0.41
117 4 0.02
118 1 0.00
120 19 0.09
121 28 0.14
122 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (114 bp):
CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTAAGCGGTCATCTTCCTGATGAGATACA
AAGAAGAATATCAACTCAGGCTCGATGTGAGCAAATCTTCAAACCCCAG
Found at i:7593 original size:206 final size:205
Alignment explanation
Indices: 7198--7682 Score: 565
Period size: 206 Copynumber: 2.4 Consensus size: 205
7188 CAAATCCCAG
* * *
7198 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTAAGGCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGAT-AAATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
* * *
7263 --A-AAGAAGA--ATATCAACTCAGGACTCGATGCGAGCAAATCTTCAAACCCCAGCTTCCTGAT
65 TGAGAAGAAGACCAAATCAACCCACGACTCGATGCGAGCAAATCTTCAAACCCCAGCTTCCTGAT
* * * * * *
7323 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGA
130 AAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAACGAAATACGGAGAAGTGA
* *
7388 ACCAAATTCGT
195 ACCAAAATCAT
* * *
7399 CTTCCTGATAATATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCTTGATGAGATTC
1 CTTCCTGATAA-ATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
* * *
7464 TGAGAAGAAGACCAAATCAAACCCACG-CTCGATGTGAGCAAATCCTT-GAACCCTAGCTTCCTG
65 TGAGAAGAAGACCAAATC-AACCCACGACTCGATGCGAGCAAAT-CTTCAAACCCCAGCTTCCTG
* * *
7527 ATAAGATACTAAGAAGCAGG-CTGAAGTAGTAAAATGGTTAGCTTCCTAACGAAATACGGGGAAG
128 ATAAGATACTAAGAAGCAGGTC-GAAGCAATAAAATGGTTAGCTTCCTAACGAAATACGGAGAAG
7591 TGAACCAAAATCAT
192 TGAACCAAAATCAT
* * ** * ** *
7605 C-TCTCTGATGAAACACAGAGAAGTGGATCAAAACAATTGATATGGTCGTCTTCCTGATGAGATA
1 CTTC-CTGAT-AAATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATA
7669 CTGAGAAGAAGACC
64 CTGAGAAGAAGACC
7683 TAGTCAATGA
Statistics
Matches: 239, Mismatches: 34, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
200 1 0.00
201 57 0.24
203 1 0.00
204 7 0.03
205 3 0.01
206 159 0.67
207 11 0.05
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (205 bp):
CTTCCTGATAAATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACT
GAGAAGAAGACCAAATCAACCCACGACTCGATGCGAGCAAATCTTCAAACCCCAGCTTCCTGATA
AGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAACGAAATACGGAGAAGTGAA
CCAAAATCAT
Found at i:8033 original size:17 final size:17
Alignment explanation
Indices: 8009--8051 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
7999 ACAGAATTTG
8009 AATTTATTTTAAAATTA
1 AATTTATTTTAAAATTA
* *
8026 AGTTTATTTTAAATTTA
1 AATTTATTTTAAAATTA
8043 AATTTATTT
1 AATTTATTT
8052 AAATAATGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
AATTTATTTTAAAATTA
Done.