Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014456.1 Kokia drynarioides strain JFW-HI SEQ_129495, 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: 19634
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1444 original size:21 final size:21
Alignment explanation
Indices: 1415--1454 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1405 ACCTTATTTT
*
1415 ATTTTACTAATAAAATAATGC
1 ATTTCACTAATAAAATAATGC
* *
1436 ATTTCACTAGTAAATTAAT
1 ATTTCACTAATAAAATAAT
1455 TTCATATATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTTCACTAATAAAATAATGC
Found at i:3446 original size:3 final size:3
Alignment explanation
Indices: 3438--3476 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3428 TTAATAAATG
3438 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3477 AAAATAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4253 original size:14 final size:15
Alignment explanation
Indices: 4230--4258 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4220 AATTTGGACA
4230 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
4245 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
4259 ATAATAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:4295 original size:6 final size:6
Alignment explanation
Indices: 4284--4344 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
4274 ATTTTGAAAA
* * *
4284 TAAATT TAAATT T-AATT TAAATT CAAATT TAAA-A TAAATC TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
4330 TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAA
4345 AGGGGCCCGG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 13 0.29
6 32 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:4302 original size:11 final size:11
Alignment explanation
Indices: 4286--4343 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
4276 TTTGAAAATA
4286 AATTTAAATTT
1 AATTTAAATTT
*
4297 AATTTAAATTCA
1 AATTTAAATT-T
* *
4309 AATTTAAAATA
1 AATTTAAATTT
*
4320 AATCTAAATTT
1 AATTTAAATTT
**
4331 AAAATAAATTT
1 AATTTAAATTT
4342 AA
1 AA
4344 AAGGGGCCCG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
11 30 0.77
12 9 0.23
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:4306 original size:17 final size:17
Alignment explanation
Indices: 4269--4344 Score: 98
Period size: 17 Copynumber: 4.4 Consensus size: 17
4259 ATAATAATCT
4269 TTTAAATTTTGAAAATAAA
1 TTTAAA-TTT-AAAATAAA
**
4288 TTTAAATTTAATTTAAA
1 TTTAAATTTAAAATAAA
*
4305 TTCAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
4322 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
4339 TTTAAA
1 TTTAAA
4345 AGGGGCCCGG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 40 0.82
18 3 0.06
19 6 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:4344 original size:11 final size:11
Alignment explanation
Indices: 4280--4345 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
4270 TTAAATTTTG
4280 AAAATAAATTT
1 AAAATAAATTT
* *
4291 AAATTTAATTT
1 AAAATAAATTT
*
4302 AAATTCAAATTT
1 AAAAT-AAATTT
4314 AAAATAAA--T
1 AAAATAAATTT
*
4323 ---CTAAATTT
1 AAAATAAATTT
4331 AAAATAAATTT
1 AAAATAAATTT
4342 AAAA
1 AAAA
4346 GGGGCCCGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
6 4 0.09
8 1 0.02
9 1 0.02
11 28 0.65
12 9 0.21
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATAAATTT
Found at i:5006 original size:206 final size:205
Alignment explanation
Indices: 4652--5457 Score: 1055
Period size: 206 Copynumber: 3.9 Consensus size: 205
4642 TTGACTTGAC
* ** * * *
4652 CTTCTTCTCAGTATCTCATGAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTTT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGA-CGCATCACTTGTTTCAATCCGCTTCTCTGTATCT
* * * *
4717 CATTAGGAAGACGGATTTGGTTCACTTCTCCGTATCTTATCAGGAAGCTAACCATTTTATTACTT
65 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
*
4782 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACATCGAGTGTGGG
130 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACATCGAGCGTGGG
4847 CTTGATTTGGT
195 CTTGATTTGGT
* * * * * *
4858 CTTCTTCTCTGTGTCTCATCAGGAAGAAGATCACATCATTTGTTTCTATCCGCTTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGA-CGCATCACTTGTTTCAATCCGCTTCTCTGTATCT
* * * *
4923 CATCAGCAAGACGAATTTGG-TCTACTTCTCAGTATCTCATCTGGAAGCTAACCTTTTTATTGCT
65 CATCAGGAAGACGAATTTGGTTC-ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACT
* * * ** * *
4987 TCGCCCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTGCATTGAACGTGG
129 TCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACATCGAGCGTGG
*
5052 GTTTGATTTGGT
194 GCTTGATTTGGT
* * * *
5064 CTTGTTCTCAGTATCTCATCAAGAAGGTGACTGCATCGCTTGTTTCAATCTC-CTTCTCTGTATC
1 CTTCTTCTCAGTATCTCATCAGGAAGATGAC-GCATCACTTGTTTCAATC-CGCTTCTCTGTATC
*
5128 TCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACT
64 TCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACT
*
5193 TTGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACATCGAGCGTGG
129 TCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACATCGAGCGTGG
5258 GCTTGATTTGGT
194 GCTTGATTTGGT
* * * * * *
5270 CTT-TCTCTCTGTGTCTCATCAGGAAGATGACCCGTCATTTGTTTCAATCCGCTTCTCTGTACCT
1 CTTCT-TCTCAGTATCTCATCAGGAAGATGACGCATCACTTGTTTCAATCCGCTTCTCTGTATCT
* * *
5334 CATCAGGAAGACGAATTTGGTCCACTTCCCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTT
65 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
* * * * * * *
5398 C-ACTCTGCTTCTCAGTATCTCATCAAGAAGCTGAGATTCAAAGATTTGCTTACTTCGAGC
130 CGAC-CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACATCGAGC
5458 CCTGATTTGG
Statistics
Matches: 519, Mismatches: 74, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
203 2 0.00
204 60 0.12
205 80 0.15
206 374 0.72
207 3 0.01
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (205 bp):
CTTCTTCTCAGTATCTCATCAGGAAGATGACGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
ATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTC
GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACATCGAGCGTGGGC
TTGATTTGGT
Found at i:5475 original size:30 final size:30
Alignment explanation
Indices: 5441--5501 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
5431 AGATTCAAAG
*
5441 ATTTGCTTACTTCGAGCCCTGATTTGGTAT
1 ATTTGCTTACATCGAGCCCTGATTTGGTAT
5471 ATTTGCTTACATCGAGCCCTGATTTGGTAT
1 ATTTGCTTACATCGAGCCCTGATTTGGTAT
5501 A
1 A
5502 CTTCTCTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (30 bp):
ATTTGCTTACATCGAGCCCTGATTTGGTAT
Found at i:11909 original size:22 final size:21
Alignment explanation
Indices: 11875--11915 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
11865 AATTCCCTGC
11875 ATCGCATCAATTTTCTCCTCTA
1 ATCGCATCAATTTT-TCCTCTA
**
11897 ATCGCATGTATTTTTCCTC
1 ATCGCATCAATTTTTCCTC
11916 CATTTGTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.29, G:0.07, T:0.44
Consensus pattern (21 bp):
ATCGCATCAATTTTTCCTCTA
Found at i:12241 original size:3 final size:3
Alignment explanation
Indices: 12233--12290 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
12223 TTAATAAATG
** *
12233 TTA TTA TTA TTA TTA TTA TTA AAA ATA GTTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A
*
12280 TAA TTA TTA TT
1 TTA TTA TTA TT
12291 GATATAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 43 0.91
4 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:12263 original size:28 final size:28
Alignment explanation
Indices: 12223--12283 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
12213 TTCCCCCTTT
12223 TTAATAAATGTTATTATTATTATTATTA
1 TTAATAAATGTTATTATTATTATTATTA
12251 TTAA-AAATAGTTATTATTATTATTATTA
1 TTAATAAAT-GTTATTATTATTATTATTA
*
12279 ATAAT
1 TTAAT
12284 TATTATTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (28 bp):
TTAATAAATGTTATTATTATTATTATTA
Found at i:12264 original size:22 final size:22
Alignment explanation
Indices: 12238--12290 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
12228 AAATGTTATT
12238 ATTATTATTATTATTAAAAATA
1 ATTATTATTATTATTAAAAATA
* **
12260 GTTATTATTATTATTATTAATA
1 ATTATTATTATTATTAAAAATA
12282 ATTATTATT
1 ATTATTATT
12291 GATATAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTATTATTATTATTAAAAATA
Found at i:13068 original size:11 final size:11
Alignment explanation
Indices: 13065--13103 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13055 AAAATAAATT
*
13065 TAAATTTAAAT
1 TAAATTTAAAA
13076 TAAATTTAAAA
1 TAAATTTAAAA
*
13087 TCAAATTGAAAA
1 T-AAATTTAAAA
13099 TAAAT
1 TAAAT
13104 CTAAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:13074 original size:17 final size:17
Alignment explanation
Indices: 13045--13125 Score: 72
Period size: 17 Copynumber: 4.4 Consensus size: 17
13035 ATAATAATCT
13045 TTTAAATTTTAAAATAAA
1 TTTAAA-TTTAAAATAAA
*
13063 TTTAAATTTAAATTAAA
1 TTTAAATTTAAAATAAA
13080 TTTAAAATCAAATTGAAAATAAA
1 TTT-AAAT----TT-AAAATAAA
* *
13103 TCTAAGTTTAAAATAAA
1 TTTAAATTTAAAATAAA
13120 TTTAAA
1 TTTAAA
13126 AGGGGCCCGA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
17 25 0.49
18 12 0.24
22 5 0.10
23 9 0.18
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:16831 original size:14 final size:15
Alignment explanation
Indices: 16803--16831 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16793 AATTTGCACA
16803 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
16818 TGTAATTT-GACTTT
1 TGTAATTTGGACTTT
16832 ATAATAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:16865 original size:11 final size:11
Alignment explanation
Indices: 16862--16900 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16852 AAAATAAATT
*
16862 TAAATTTAAAT
1 TAAATTTAAAA
16873 TAAATTTAAAA
1 TAAATTTAAAA
*
16884 TCAAATTGAAAA
1 T-AAATTTAAAA
16896 TAAAT
1 TAAAT
16901 CTAAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:16871 original size:17 final size:17
Alignment explanation
Indices: 16842--16922 Score: 72
Period size: 17 Copynumber: 4.4 Consensus size: 17
16832 ATAATAATCT
16842 TTTAAATTTTAAAATAAA
1 TTTAAA-TTTAAAATAAA
*
16860 TTTAAATTTAAATTAAA
1 TTTAAATTTAAAATAAA
16877 TTTAAAATCAAATTGAAAATAAA
1 TTT-AAAT----TT-AAAATAAA
* *
16900 TCTAAGTTTAAAATAAA
1 TTTAAATTTAAAATAAA
16917 TTTAAA
1 TTTAAA
16923 AGGGCCTGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
17 25 0.49
18 12 0.24
22 5 0.10
23 9 0.18
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Done.