Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011036.1 Kokia drynarioides strain JFW-HI SEQ_126007, 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: 44272
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:479 original size:27 final size:27
Alignment explanation
Indices: 430--604 Score: 135
Period size: 27 Copynumber: 7.0 Consensus size: 27
420 ACGATCGACA
*
430 GAGAAGATG-GATTGGAGAAGGAGAAT
1 GAGAAGCTGAGATTGGAGAAGGAGAAT
* * **
456 GCGAGGCTGAGATTGGAGTTGGAGAAT
1 GAGAAGCTGAGATTGGAGAAGGAGAAT
*
483 GAGAAGCTGAGATT------GGAGAAC
1 GAGAAGCTGAGATTGGAGAAGGAGAAT
504 GAGAAGCTGAGATTGGAGAA------T
1 GAGAAGCTGAGATTGGAGAAGGAGAAT
** *
525 GAGAAGCTGAGATTGGAGTTGGAGAAC
1 GAGAAGCTGAGATTGGAGAAGGAGAAT
* *
552 GAGAAGCTTAGATTGGAGTTA-GAGAAT
1 GAGAAGCTGAGATTGGAG-AAGGAGAAT
*
579 GAGAAGCTGAGATTGGAGAACGAGAA
1 GAGAAGCTGAGATTGGAGAAGGAGAA
605 GCTGAGATTG
Statistics
Matches: 117, Mismatches: 17, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
21 38 0.32
26 7 0.06
27 71 0.61
28 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.39, T:0.18
Consensus pattern (27 bp):
GAGAAGCTGAGATTGGAGAAGGAGAAT
Found at i:513 original size:48 final size:48
Alignment explanation
Indices: 461--639 Score: 216
Period size: 48 Copynumber: 3.9 Consensus size: 48
451 AGAATGCGAG
461 GCTGAGATTGGAGTTGGAGAATGAGAAGCTGAGATTGGAGAACGAGAA
1 GCTGAGATTGGAGTTGGAGAATGAGAAGCTGAGATTGGAGAACGAGAA
* *
509 GCTGAGATTGGAGAAT-GAGAAGCTGAG-A-TTG-GAGTTGGAGAACGAGAA
1 GCTGAGATTGGAG-TTGGAGAA--TGAGAAGCTGAGA-TTGGAGAACGAGAA
* *
557 GCTTAGATTGGAGTTAGAGAATGAGAAGCTGAGATTGGAGAACGAGAA
1 GCTGAGATTGGAGTTGGAGAATGAGAAGCTGAGATTGGAGAACGAGAA
605 GCT--GA---GA-TTGGAGAATGAGAAGCTGAGATTGGAGA
1 GCTGAGATTGGAGTTGGAGAATGAGAAGCTGAGATTGGAGA
640 TAGAGACGCT
Statistics
Matches: 117, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
42 27 0.23
43 2 0.02
46 6 0.05
47 4 0.03
48 70 0.60
49 4 0.03
50 4 0.03
ACGTcount: A:0.36, C:0.06, G:0.39, T:0.20
Consensus pattern (48 bp):
GCTGAGATTGGAGTTGGAGAATGAGAAGCTGAGATTGGAGAACGAGAA
Found at i:549 original size:96 final size:96
Alignment explanation
Indices: 430--639 Score: 341
Period size: 96 Copynumber: 2.2 Consensus size: 96
420 ACGATCGACA
* * * * *
430 GAGAAGATG-GATTGGAGAAGGAGAATGCGAGGCTGAGATTGGAGTTGGAGAATGAGAAGCTGAG
1 GAGAAGCTGAGATTGGAGAAGGAGAACGAGAAGCTGAGATTGGAGTTAGAGAATGAGAAGCTGAG
494 ATTGGAGAACGAGAAGCTGAGATTGGAGAAT
66 ATTGGAGAACGAGAAGCTGAGATTGGAGAAT
** *
525 GAGAAGCTGAGATTGGAGTTGGAGAACGAGAAGCTTAGATTGGAGTTAGAGAATGAGAAGCTGAG
1 GAGAAGCTGAGATTGGAGAAGGAGAACGAGAAGCTGAGATTGGAGTTAGAGAATGAGAAGCTGAG
590 ATTGGAGAACGAGAAGCTGAGATTGGAGAAT
66 ATTGGAGAACGAGAAGCTGAGATTGGAGAAT
621 GAGAAGCTGAGATTGGAGA
1 GAGAAGCTGAGATTGGAGA
640 TAGAGACGCT
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
95 8 0.08
96 97 0.92
ACGTcount: A:0.36, C:0.06, G:0.40, T:0.19
Consensus pattern (96 bp):
GAGAAGCTGAGATTGGAGAAGGAGAACGAGAAGCTGAGATTGGAGTTAGAGAATGAGAAGCTGAG
ATTGGAGAACGAGAAGCTGAGATTGGAGAAT
Found at i:645 original size:21 final size:21
Alignment explanation
Indices: 474--639 Score: 188
Period size: 21 Copynumber: 7.3 Consensus size: 21
464 GAGATTGGAG
474 TTGGAGAATGAGAAGCTGAGA
1 TTGGAGAATGAGAAGCTGAGA
*
495 TTGGAGAACGAGAAGCTGAGA
1 TTGGAGAATGAGAAGCTGAGA
516 TTGGAGAATGAGAAGCTGAGATTGGA
1 TTGGAGAATGAGAAGCT--GA---GA
* *
542 GTTGGAGAACGAGAAGCTTAGA
1 -TTGGAGAATGAGAAGCTGAGA
564 TTGGAGTTAGAGAATGAGAAGCTGAGA
1 TT---G---GAGAATGAGAAGCTGAGA
*
591 TTGGAGAACGAGAAGCTGAGA
1 TTGGAGAATGAGAAGCTGAGA
612 TTGGAGAATGAGAAGCTGAGA
1 TTGGAGAATGAGAAGCTGAGA
633 TTGGAGA
1 TTGGAGA
640 TAGAGACGCT
Statistics
Matches: 125, Mismatches: 8, Indels: 24
0.80 0.05 0.15
Matches are distributed among these distances:
21 82 0.66
22 2 0.02
23 2 0.02
24 2 0.02
25 1 0.01
26 2 0.02
27 34 0.27
ACGTcount: A:0.37, C:0.06, G:0.38, T:0.19
Consensus pattern (21 bp):
TTGGAGAATGAGAAGCTGAGA
Found at i:4753 original size:3 final size:3
Alignment explanation
Indices: 4745--4780 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4735 TAGACCTTAA
4745 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4781 CATTAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6696 original size:2 final size:2
Alignment explanation
Indices: 6653--6682 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6643 TTGATTAATA
6653 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6683 AATGAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19317 original size:51 final size:51
Alignment explanation
Indices: 19198--19536 Score: 513
Period size: 51 Copynumber: 6.6 Consensus size: 51
19188 TTTCATTTAA
* * * *
19198 TACTCACGATGACA-TATAGTCATCGGACCTCTT-GTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATT-CGTAAAGG-ATTCATT
* *
19251 GACTCACGATGACACTTAGTCATTGGACCTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
19302 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
* *
19353 TACTCACGATGACACTTAGTCATCGAACTTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
* * *
19404 TACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAATGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
*
19455 TACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
19506 TACTCACGATGACACTTAGT-ATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
19537 TCGTTTATAG
Statistics
Matches: 264, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
50 10 0.04
51 217 0.82
52 8 0.03
53 28 0.11
54 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
Found at i:24921 original size:22 final size:23
Alignment explanation
Indices: 24883--24934 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
24873 CTCTGTTTAT
*
24883 TTAGCACGTATTGTGCTCTTCGA
1 TTAGCACGTATTGTGCTCTCCGA
*
24906 TTAGCACGT-TTGTGCTCTCCGT
1 TTAGCACGTATTGTGCTCTCCGA
24928 TTAGCAC
1 TTAGCAC
24935 CCCGGTGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.38
Consensus pattern (23 bp):
TTAGCACGTATTGTGCTCTCCGA
Found at i:35449 original size:27 final size:29
Alignment explanation
Indices: 35419--35472 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
35409 TTAATAAAGA
35419 ATTTAAAATAATT-AAT-A-TTTTATTTCG
1 ATTTAAAA-AATTGAATAATTTTTATTTCG
35446 ATTTAAAAAATTGAATAATTTTTATTT
1 ATTTAAAAAATTGAATAATTTTTATTT
35473 TGTCAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.17
27 11 0.46
28 1 0.04
29 8 0.33
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (29 bp):
ATTTAAAAAATTGAATAATTTTTATTTCG
Found at i:42988 original size:21 final size:21
Alignment explanation
Indices: 42944--42990 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
42934 TTTATAAAGT
* *
42944 TAAAAATTAATATAAGAAATA
1 TAAAAATTAATATAACAAAAA
42965 TAAAAATTAAT-TCAACAAAAA
1 TAAAAATTAATAT-AACAAAAA
42986 TAAAA
1 TAAAA
42991 TACTAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAATTAATATAACAAAAA
Found at i:43004 original size:20 final size:19
Alignment explanation
Indices: 42978--43032 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
42968 AAATTAATTC
42978 AACAAAAATAAAATACTAA
1 AACAAAAATAAAATACTAA
* *
42997 AACTAAAATTAAAATCTCTAA
1 AAC-AAAAATAAAAT-ACTAA
*
43018 AGCAAAAATAAAATA
1 AACAAAAATAAAATA
43033 TATATAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.10
20 20 0.69
21 6 0.21
ACGTcount: A:0.67, C:0.11, G:0.02, T:0.20
Consensus pattern (19 bp):
AACAAAAATAAAATACTAA
Found at i:43791 original size:29 final size:29
Alignment explanation
Indices: 43754--43809 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
43744 ACCATGACAA
* *
43754 GAATTCTCAACGAACAAGTTCTTCACCAT
1 GAATGCTCAACGAACAAGTTCTCCACCAT
43783 GAATGCTCAACGAACAAGTTCTCCACC
1 GAATGCTCAACGAACAAGTTCTCCACC
43810 TCTCCATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.23
Consensus pattern (29 bp):
GAATGCTCAACGAACAAGTTCTCCACCAT
Found at i:44158 original size:6 final size:6
Alignment explanation
Indices: 44147--44242 Score: 83
Period size: 6 Copynumber: 16.7 Consensus size: 6
44137 ATTTGTTTAA
* * *
44147 AAATTT AAATTT -ATTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* ** * * *
44193 -AATTT AAGTTT AAATTT ATTTTT AAATTT AAAATT -ACTAT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
44239 AAAT
1 AAAT
44243 AAAGCTAAAA
Statistics
Matches: 69, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
5 15 0.22
6 54 0.78
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:44166 original size:11 final size:11
Alignment explanation
Indices: 44167--44222 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
44157 TTATTTTAAA
44167 TTTAAATTTAT
1 TTTAAATTTAT
* *
44178 TTTGAATTTAAA
1 TTTAAATTT-AT
*
44190 TTT-AATTTAAG
1 TTTAAATTT-AT
44201 TTTAAATTTATT
1 TTTAAATTTA-T
44213 TTTAAATTTA
1 TTTAAATTTA
44223 AAATTACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 19 0.50
12 19 0.50
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:44173 original size:23 final size:24
Alignment explanation
Indices: 44147--44242 Score: 83
Period size: 23 Copynumber: 4.2 Consensus size: 24
44137 ATTTGTTTAA
*
44147 AAATTTAAATTT-ATTTTAAATTT
1 AAATTTAAATTTAAATTTAAATTT
* *
44170 AAATTT-ATTTTGAATTTAAATTT
1 AAATTTAAATTTAAATTTAAATTT
* **
44193 -AATTTAAGTTTAAATTTATTTTT
1 AAATTTAAATTTAAATTTAAATTT
* * *
44216 AAATTTAAAATT-ACTATAAATTT
1 AAATTTAAATTTAAATTTAAATTT
44239 AAAT
1 AAAT
44243 AAAGCTAAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
22 9 0.16
23 40 0.69
24 9 0.16
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (24 bp):
AAATTTAAATTTAAATTTAAATTT
Found at i:44237 original size:17 final size:17
Alignment explanation
Indices: 44114--44242 Score: 150
Period size: 17 Copynumber: 7.4 Consensus size: 17
44104 CCGAACTCCC
44114 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
44132 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
44150 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
44167 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
* *
44184 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
44201 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* * *
44219 TTTAAAATTACTATAAA
1 TTTAAATTTATTTTAAA
44236 TTTAAAT
1 TTTAAAT
44243 AAAGCTAAAA
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
17 54 0.58
18 39 0.42
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:44240 original size:35 final size:35
Alignment explanation
Indices: 44114--44242 Score: 143
Period size: 35 Copynumber: 3.7 Consensus size: 35
44104 CCGAACTCCC
* * * **
44114 TTTAAATTTATTTTAAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTAATTT-AAATTTAAATTTATTTTTAAA
* *
44150 TTTAAATTTATTTTAAATTTAAATTTA-TTTTGAA
1 TTTAAATTTAATTTAAATTTAAATTTATTTTTAAA
*
44184 TTTAAATTTAATTTAAGTTTAAATTTATTTTTAAA
1 TTTAAATTTAATTTAAATTTAAATTTATTTTTAAA
* * *
44219 TTTAAAATTACTATAAATTTAAAT
1 TTTAAATTTAATTTAAATTTAAAT
44243 AAAGCTAAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
34 29 0.36
35 37 0.46
36 14 0.17
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (35 bp):
TTTAAATTTAATTTAAATTTAAATTTATTTTTAAA
Done.