Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005082.1 Kokia drynarioides strain JFW-HI SEQ_118892, 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: 61338
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:8655 original size:30 final size:30
Alignment explanation
Indices: 8619--8678 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
8609 AAGAAGAAAG
8619 ACTTATGAAAAAGAATGTTGGTAGAGCTCT
1 ACTTATGAAAAAGAATGTTGGTAGAGCTCT
*
8649 ACTTATGAAGAAGAATGTTGGTAGAGCTCT
1 ACTTATGAAAAAGAATGTTGGTAGAGCTCT
8679 TAAATCCACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (30 bp):
ACTTATGAAAAAGAATGTTGGTAGAGCTCT
Found at i:13036 original size:31 final size:31
Alignment explanation
Indices: 12966--13038 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
12956 TTTGTCCAAT
* *
12966 TTGGTACTCAAACTTGACACTTTTTCTTAAT
1 TTGGTACTTAAACTTGACACTTTTTCTTAAG
* *
12997 TTGATACTTAAACTTGACA-TTTATTTTTAAG
1 TTGGTACTTAAACTTGACACTTT-TTCTTAAG
13028 TTGGTACTTAA
1 TTGGTACTTAA
13039 GCTTTTTAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 3 0.08
31 33 0.92
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.47
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACTTTTTCTTAAG
Found at i:13364 original size:59 final size:62
Alignment explanation
Indices: 13245--13375 Score: 169
Period size: 59 Copynumber: 2.2 Consensus size: 62
13235 TAATAAATTT
13245 AGGTACCAAATTGAATCTAAAAAAAATCTTAGGTACCAAATTAGGAAAAAAATATCAAGTTC
1 AGGTACCAAATTGAATCTAAAAAAAATCTTAGGTACCAAATTAGGAAAAAAATATCAAGTTC
* ** * ** *
13307 AGGTACGAAATTGGGTC-AAAAAAAGT-TTAGGTACCAAATTA-GAAAAAGGTGTCAAGTTC
1 AGGTACCAAATTGAATCTAAAAAAAATCTTAGGTACCAAATTAGGAAAAAAATATCAAGTTC
*
13366 AAGTACCAAA
1 AGGTACCAAA
13376 AGTTATATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
59 23 0.38
60 15 0.25
61 8 0.13
62 14 0.23
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (62 bp):
AGGTACCAAATTGAATCTAAAAAAAATCTTAGGTACCAAATTAGGAAAAAAATATCAAGTTC
Found at i:18403 original size:20 final size:20
Alignment explanation
Indices: 18366--18421 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
18356 CTACCCTGGG
* *
18366 ACTTCTACCGGTAGAACTTC
1 ACTTCTACCGATACAACTTC
* *
18386 ACTTTTACTGATACAACTTC
1 ACTTCTACCGATACAACTTC
*
18406 AGTTCTACCGATACAA
1 ACTTCTACCGATACAA
18422 GTATGCTTCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (20 bp):
ACTTCTACCGATACAACTTC
Found at i:24199 original size:21 final size:20
Alignment explanation
Indices: 24162--24200 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
24152 TGGGTCTGAT
*
24162 AAATAGATAAACGTTATGAC
1 AAATAGATAAAAGTTATGAC
*
24182 AAATGAGATAAAATTTATG
1 AAAT-AGATAAAAGTTATG
24201 GAACAAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.28
Consensus pattern (20 bp):
AAATAGATAAAAGTTATGAC
Found at i:26146 original size:43 final size:43
Alignment explanation
Indices: 26093--26238 Score: 163
Period size: 43 Copynumber: 3.4 Consensus size: 43
26083 TGGGTTTATA
* *
26093 CTTTGTTTTATTCGATGATGCTCTATGTGTGCTAGTATGATTG
1 CTTTGATTTATTCGATGATGCACTATGTGTGCTAGTATGATTG
* *
26136 CTTTGATTTATCCGATGATGCACTATGTGTGCCAGTATGATTG
1 CTTTGATTTATTCGATGATGCACTATGTGTGCTAGTATGATTG
* * *
26179 CTTCGATTT-TTCCAATGATGCACCT-TGTGTGCTAGTATAATTG
1 CTTTGATTTATT-CGATGATGCA-CTATGTGTGCTAGTATGATTG
* *
26222 -TTTCGGTTTGTTCGATG
1 CTTT-GATTTATTCGATG
26239 GTACACCTCG
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
42 3 0.03
43 80 0.92
44 4 0.05
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.45
Consensus pattern (43 bp):
CTTTGATTTATTCGATGATGCACTATGTGTGCTAGTATGATTG
Found at i:26289 original size:43 final size:43
Alignment explanation
Indices: 26193--26296 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
26183 GATTTTTCCA
* * * *
26193 ATGATGCACCTTGTGTGCTAGTATAATTGTTTCGGTTTGTTCG
1 ATGATGCACCTCGTGTGCTAATATAATTCTTTCGGTTCGTTCG
* * *
26236 ATGGTACACCTCGTGTGCTAATATAATTACTTT-GGTTCGTTTG
1 ATGATGCACCTCGTGTGCTAATATAATT-CTTTCGGTTCGTTCG
*
26279 ATGATGCACCTCATGTGC
1 ATGATGCACCTCGTGTGC
26297 CAGTATATCT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 47 0.94
44 3 0.06
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (43 bp):
ATGATGCACCTCGTGTGCTAATATAATTCTTTCGGTTCGTTCG
Found at i:29156 original size:31 final size:30
Alignment explanation
Indices: 29114--29205 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
29104 TATCGATGAC
* *
29114 TATATTATATCAGGAACTATGTATTGGTGTT
1 TATATTTTATCA-GAACTATGTATCGGTGTT
* * *
29145 TAT-TTTGTATCATACACAATGTGTCGGTGTT
1 TATATTT-TATCAGA-ACTATGTATCGGTGTT
* *
29176 TATATTTTATCAAGTACTATGTATCAGTGT
1 TATATTTTATC-AGAACTATGTATCGGTGT
29206 CAGACACCTT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
30 3 0.06
31 40 0.85
32 4 0.09
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (30 bp):
TATATTTTATCAGAACTATGTATCGGTGTT
Found at i:30478 original size:1 final size:1
Alignment explanation
Indices: 30474--30501 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
30464 TTTTCCTTAA
30474 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
30502 GATTTAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:32206 original size:24 final size:24
Alignment explanation
Indices: 32127--32206 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
32117 AAAGTAAAAC
* *
32127 ATAAAA-AAAAATTATGTTTTAAAA
1 ATAAAATAAAAAATAT-TTTTAAAT
* *
32151 ATAATAATAAAAAACT-CTTTAAAATT
1 ATAA-AATAAAAAA-TATTTTTAAA-T
*
32177 AAAAAATAAAAAATATTTTTAAAT
1 ATAAAATAAAAAATATTTTTAAAT
32201 ATAAAA
1 ATAAAA
32207 AAATTTCTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
24 11 0.26
25 23 0.53
26 8 0.19
27 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.33
Consensus pattern (24 bp):
ATAAAATAAAAAATATTTTTAAAT
Found at i:32212 original size:18 final size:19
Alignment explanation
Indices: 32182--32217 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
32172 AAATTAAAAA
*
32182 ATAAAAAATATTTTTAAAT
1 ATAAAAAATATTTCTAAAT
32201 ATAAAAAA-ATTTCTAAA
1 ATAAAAAATATTTCTAAA
32218 ATTCAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAAAAATATTTCTAAAT
Found at i:32219 original size:19 final size:19
Alignment explanation
Indices: 32175--32219 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
32165 CTCTTTAAAA
*
32175 TTAAAAAATAAAAAATATT
1 TTAAAATATAAAAAATATT
*
32194 TTTAAATATAAAAAA-ATT
1 TTAAAATATAAAAAATATT
32212 TCTAAAAT
1 T-TAAAAT
32220 TCAATATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAATATAAAAAATATT
Found at i:32445 original size:18 final size:19
Alignment explanation
Indices: 32418--32455 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
32408 AATAAACTAA
*
32418 ATTATTAAAA-ATAAAAAT
1 ATTATAAAAACATAAAAAT
32436 ATTATAAAAACTATAAAAAT
1 ATTATAAAAAC-ATAAAAAT
32456 CGATCTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTATAAAAACATAAAAAT
Found at i:34301 original size:86 final size:86
Alignment explanation
Indices: 34152--34331 Score: 297
Period size: 86 Copynumber: 2.1 Consensus size: 86
34142 TTGACTAAAT
* ** *
34152 TATTACTATTTATGCATGGTATGTAATTAGTACATGCCTTCTTTGATTGGATTACTGAGTAGTTG
1 TATTACTATATATGCATGGTATGTAATTAGTACATGCCTTCTTTGATTGGACGACTAAGTAGTTG
34217 TTACTGATACTCGAACCACTA
66 TTACTGATACTCGAACCACTA
* * *
34238 TATTACTATATATGCATGGTATGTAATTAGTACATGCCTTTTTTGTTTGGACGACTAATTAGTTG
1 TATTACTATATATGCATGGTATGTAATTAGTACATGCCTTCTTTGATTGGACGACTAAGTAGTTG
34303 TTACTGATACTCGAACCACTA
66 TTACTGATACTCGAACCACTA
34324 TATTACTA
1 TATTACTA
34332 ATTGTATGAA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (86 bp):
TATTACTATATATGCATGGTATGTAATTAGTACATGCCTTCTTTGATTGGACGACTAAGTAGTTG
TTACTGATACTCGAACCACTA
Found at i:41272 original size:68 final size:68
Alignment explanation
Indices: 41192--41335 Score: 261
Period size: 68 Copynumber: 2.1 Consensus size: 68
41182 TAATGGGAAA
41192 TCACATAATGGGAAGTGAAAGCTCAACAACAAACCAAAAGGGCTAGTGGAATGCTTCATTTGTAA
1 TCACATAATGGGAAGTGAAAGCTCAACAACAAACCAAAAGGGCTAGTGGAATGCTTCATTTGTAA
41257 CGG
66 CGG
* *
41260 TCACATAATGGGAAGTGGAAGCTCAACAACAAACCAAAAGGGCTAGTGGAATGCTTCATTTGTGA
1 TCACATAATGGGAAGTGAAAGCTCAACAACAAACCAAAAGGGCTAGTGGAATGCTTCATTTGTAA
41325 CGG
66 CGG
41328 TCCACATA
1 T-CACATA
41336 TGGTGAGGGA
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 67 0.92
69 6 0.08
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.21
Consensus pattern (68 bp):
TCACATAATGGGAAGTGAAAGCTCAACAACAAACCAAAAGGGCTAGTGGAATGCTTCATTTGTAA
CGG
Found at i:44426 original size:21 final size:21
Alignment explanation
Indices: 44400--44440 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
44390 GTGTACATTC
* *
44400 AAAAATATGACTTTTTTTTTT
1 AAAAATATGAATATTTTTTTT
*
44421 AAAAATTTGAATATTTTTTT
1 AAAAATATGAATATTTTTTT
44441 ATCGTGAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (21 bp):
AAAAATATGAATATTTTTTTT
Found at i:46522 original size:18 final size:18
Alignment explanation
Indices: 46496--46530 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
46486 GTAGAATTGA
46496 TTTTCTTTATTTTTTATT
1 TTTTCTTTATTTTTTATT
*
46514 TTTTTTTTATTTTTTAT
1 TTTTCTTTATTTTTTAT
46531 CACCAAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTCTTTATTTTTTATT
Found at i:53490 original size:16 final size:17
Alignment explanation
Indices: 53469--53500 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
53459 ACATAAAAAA
53469 TAAAAATATA-AATTTT
1 TAAAAATATATAATTTT
53485 TAAAAATATATAATTT
1 TAAAAATATATAATTT
53501 ATAATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAAATATATAATTTT
Found at i:53525 original size:23 final size:24
Alignment explanation
Indices: 53462--53525 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
53452 ACATAAAACA
53462 TAAAAAA-TAAAAA-TATAAATTT
1 TAAAAAATTAAAAATTATAAATTT
* * *
53484 TTAAAAATATATAATTTAT-AATTT
1 TAAAAAAT-TAAAAATTATAAATTT
53508 TAAAAAATTAAAAATTAT
1 TAAAAAATTAAAAATTAT
53526 GAAAAAAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
22 6 0.18
23 8 0.24
24 16 0.48
25 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAAAAATTAAAAATTATAAATTT
Found at i:54306 original size:77 final size:77
Alignment explanation
Indices: 54214--54368 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
54204 AGAGAGAAAA
54214 TCTTGCATGCTCAAGTTTCCACCATTGCCGTCCTTCATCCATAGAGGTTTAACAATGTTGTTGAG
1 TCTTGCATGCTCAAGTTTCCACCATTGCCGTCCTTCATCCATAGAGGTTTAACAATGTTGTTGAG
54279 GAAGGTTATTCT
66 GAAGGTTATTCT
54291 TCTTGCATGCTCAAGTTTCCACCATTGCCGTCCTTCATCCATAGAGGTTTAACAATGTTGTTGAG
1 TCTTGCATGCTCAAGTTTCCACCATTGCCGTCCTTCATCCATAGAGGTTTAACAATGTTGTTGAG
54356 GAAGGTTATTCT
66 GAAGGTTATTCT
54368 T
1 T
54369 TGAGCTTGTC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (77 bp):
TCTTGCATGCTCAAGTTTCCACCATTGCCGTCCTTCATCCATAGAGGTTTAACAATGTTGTTGAG
GAAGGTTATTCT
Found at i:56352 original size:25 final size:23
Alignment explanation
Indices: 56320--56365 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
56310 GTTGGATCCA
56320 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
56345 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
56366 CCCTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:59197 original size:2 final size:2
Alignment explanation
Indices: 59190--59224 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
59180 TTAATTAATA
59190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59225 TATTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.