Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015240.1 Kokia drynarioides strain JFW-HI SEQ_130285, 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: 123831
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 301 characters in sequence are not A, C, G, or T
Found at i:7603 original size:20 final size:20
Alignment explanation
Indices: 7573--7612 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
7563 CGTAGTATTA
7573 GATTTTTTAGT-AATGGGAG
1 GATTTTTTAGTCAATGGGAG
7592 GATTTGTTTAGTCAATGGGAG
1 GATTT-TTTAGTCAATGGGAG
7613 TAGTTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
21 8 0.42
ACGTcount: A:0.25, C:0.03, G:0.33, T:0.40
Consensus pattern (20 bp):
GATTTTTTAGTCAATGGGAG
Found at i:21884 original size:23 final size:23
Alignment explanation
Indices: 21858--21904 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
21848 AAATGCATGG
21858 TATAACTCGATGAAATTATGTTA
1 TATAACTCGATGAAATTATGTTA
21881 TATAACTCGATGAAATTATGTTA
1 TATAACTCGATGAAATTATGTTA
21904 T
1 T
21905 TGCTCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
TATAACTCGATGAAATTATGTTA
Found at i:26258 original size:6 final size:6
Alignment explanation
Indices: 26235--26271 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
26225 CCTCTTGGCC
* *
26235 GTCCTG GCCCTC GTCCTG GTCCTG GTCCTG GTCCTG G
1 GTCCTG GTCCTG GTCCTG GTCCTG GTCCTG GTCCTG G
26272 ACCACTGGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.32, T:0.30
Consensus pattern (6 bp):
GTCCTG
Found at i:28860 original size:40 final size:39
Alignment explanation
Indices: 28770--28860 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 39
28760 ACAGTAAAAT
* *
28770 TTAAAATTTTATTATTTTAATAAATTTTAAATGATTAAA
1 TTAAAATTTTATCATTTTAATAAATTTTAAATGACTAAA
* * * * *
28809 TCAAATTTTTATCATTTT-TTATAATTTTATCATTACTAAA
1 TTAAAATTTTATCATTTTAATA-AATTTTA-AATGACTAAA
28849 TTAAAATTTTAT
1 TTAAAATTTTAT
28861 AAATTATAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
38 2 0.05
39 22 0.54
40 17 0.41
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (39 bp):
TTAAAATTTTATCATTTTAATAAATTTTAAATGACTAAA
Found at i:31576 original size:38 final size:38
Alignment explanation
Indices: 31487--31575 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
31477 AAAAAATATA
* * *
31487 TTTAATACAATAAAATATTTATTATATTTATTTATGTT
1 TTTAATATAATAAAACATTTATTATATTTATATATGTT
31525 TTTAATATAATAAAACATTTATTATATTTATGATAGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTAT-ATA-TG-TT
31566 TTTAATATAA
1 TTTAATATAA
31576 ATACTTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 29 0.64
39 2 0.04
40 2 0.04
41 12 0.27
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (38 bp):
TTTAATATAATAAAACATTTATTATATTTATATATGTT
Found at i:32315 original size:12 final size:12
Alignment explanation
Indices: 32300--32416 Score: 75
Period size: 12 Copynumber: 10.2 Consensus size: 12
32290 GCTTTTTTTA
*
32300 TTGTTTTGGTTG
1 TTGTTTTTGTTG
*
32312 TTGTTTTCG-TG
1 TTGTTTTTGTTG
* *
32323 TTGTTTTTGCTA
1 TTGTTTTTGTTG
*
32335 TTATTTTTGTTG
1 TTGTTTTTGTTG
*
32347 -T-TATTT-TTG
1 TTGTTTTTGTTG
**
32356 TTGTTTTTAATG
1 TTGTTTTTGTTG
*
32368 TTG-TTTTGCTG
1 TTGTTTTTGTTG
*
32379 TTATTTTTGTTG
1 TTGTTTTTGTTG
*
32391 CTG-TTTTGATTG
1 TTGTTTTTG-TTG
*
32403 TTATTTTTGTTG
1 TTGTTTTTGTTG
32415 TT
1 TT
32417 TGAATGTTAT
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
9 3 0.04
10 5 0.06
11 28 0.35
12 40 0.49
13 5 0.06
ACGTcount: A:0.07, C:0.03, G:0.21, T:0.69
Consensus pattern (12 bp):
TTGTTTTTGTTG
Found at i:32318 original size:20 final size:18
Alignment explanation
Indices: 32265--32318 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
32255 TTACTAATTT
32265 TTTTGTTGTTTTTTAATG
1 TTTTGTTGTTTTTTAATG
* *
32283 TTTTGATGCTTTTTTTATTG
1 TTTTGTTG--TTTTTTAATG
32303 TTTTGGTTGTTGTTTT
1 TTTT-GTTGTT-TTTT
32319 CGTGTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 7 0.24
19 2 0.07
20 17 0.59
21 3 0.10
ACGTcount: A:0.07, C:0.02, G:0.19, T:0.72
Consensus pattern (18 bp):
TTTTGTTGTTTTTTAATG
Found at i:32359 original size:15 final size:15
Alignment explanation
Indices: 32323--32395 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 15
32313 TGTTTTCGTG
* *
32323 TTGTTTTTGCTATTAT
1 TTGTTGTTGTTATT-T
32339 TT-TTGTTGTTATTT
1 TTGTTGTTGTTATTT
*
32353 TTGTTGTTTTTAATGTT
1 TTGTTGTTGTT-AT-TT
*
32370 GTT-TTGCTGTTATTT
1 -TTGTTGTTGTTATTT
*
32385 TTGTTGCTGTT
1 TTGTTGTTGTT
32396 TTGATTGTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.11
15 26 0.55
16 6 0.13
17 8 0.17
18 2 0.04
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (15 bp):
TTGTTGTTGTTATTT
Found at i:32370 original size:56 final size:56
Alignment explanation
Indices: 32280--32417 Score: 142
Period size: 56 Copynumber: 2.5 Consensus size: 56
32270 TTGTTTTTTA
* *** * *
32280 ATGTTTTGA-TGCTT-TTTTTATTGTTTTGGTTGTTGTTTTCG-TGTTGTTTTTGCTATT
1 ATGTTTTGATTG-TTATTTTTGTTGTTTTTAATGTTGTTTT-GCTGTTATTTTTG-T-TG
32337 AT-TTTTG-TTGTTATTTTTGTTGTTTTTAATGTTGTTTTGCTGTTATTTTTGTTG
1 ATGTTTTGATTGTTATTTTTGTTGTTTTTAATGTTGTTTTGCTGTTATTTTTGTTG
*
32391 CTGTTTTGATTGTTATTTTTGTTGTTT
1 ATGTTTTGATTGTTATTTTTGTTGTTT
32418 GAATGTTATT
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
54 2 0.03
55 9 0.13
56 56 0.81
57 2 0.03
ACGTcount: A:0.08, C:0.04, G:0.20, T:0.69
Consensus pattern (56 bp):
ATGTTTTGATTGTTATTTTTGTTGTTTTTAATGTTGTTTTGCTGTTATTTTTGTTG
Found at i:32387 original size:44 final size:43
Alignment explanation
Indices: 32262--32430 Score: 127
Period size: 44 Copynumber: 3.9 Consensus size: 43
32252 TGGTTACTAA
* *
32262 TTTTTTTGTTGTTTTTTAA---TGTTTTGATGCTT-TTTTTATTG
1 TTTTTTTGTTG-TTTTTAATGTTGTTTTGCTG-TTATTTTTGTTG
* ** *
32303 TTTTGGTTGTTG-TTTTCGTGTTGTTTTTGCTATTATTTTTGTTG
1 TTTT-TTTGTTGTTTTTAATGTTG-TTTTGCTGTTATTTTTGTTG
32347 TTATTTTTGTTGTTTTTAATGTTGTTTTGCTGTTATTTTTGTTG
1 TT-TTTTTGTTGTTTTTAATGTTGTTTTGCTGTTATTTTTGTTG
* * * *
32391 CTGTTTTGATTGTTATTT-TTGTTG-TTTGAATGTTATTTTT
1 TTTTTTTG-TTGTT-TTTAATGTTGTTTTG-CTGTTATTTTT
32431 TTATGCGTTT
Statistics
Matches: 103, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
40 4 0.04
41 4 0.04
42 6 0.06
43 13 0.13
44 62 0.60
45 14 0.14
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (43 bp):
TTTTTTTGTTGTTTTTAATGTTGTTTTGCTGTTATTTTTGTTG
Found at i:32430 original size:21 final size:22
Alignment explanation
Indices: 32369--32431 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 22
32359 TTTTTAATGT
*
32369 TGTTTTG-CTGTTATTTTTGTTGC
1 TGTTTTGAATGTTA-TTTT-TTGC
* *
32392 TGTTTTGATTGTTA-TTTTTGT
1 TGTTTTGAATGTTATTTTTTGC
32413 TG-TTTGAATGTTATTTTTT
1 TGTTTTGAATGTTATTTTTT
32432 TATGCGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 10 0.29
21 10 0.29
22 3 0.09
23 7 0.20
24 5 0.14
ACGTcount: A:0.10, C:0.03, G:0.19, T:0.68
Consensus pattern (22 bp):
TGTTTTGAATGTTATTTTTTGC
Found at i:37511 original size:25 final size:25
Alignment explanation
Indices: 37450--37503 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
37440 GGAAGTACTT
37450 AACAGAAG-AGCATAAGTGCTGGGGA
1 AACAGAAGCA-CATAAGTGCTGGGGA
37475 AACAGAAGCACATAAGTGCT-GGGA
1 AACAGAAGCACATAAGTGCTGGGGA
37499 AACAG
1 AACAG
37504 TAGGCACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 9 0.32
25 18 0.64
26 1 0.04
ACGTcount: A:0.43, C:0.15, G:0.31, T:0.11
Consensus pattern (25 bp):
AACAGAAGCACATAAGTGCTGGGGA
Found at i:37537 original size:22 final size:22
Alignment explanation
Indices: 37475--37575 Score: 96
Period size: 22 Copynumber: 4.4 Consensus size: 22
37465 GTGCTGGGGA
*
37475 AACAGAAGCACATA-AGTGCTGGG
1 AACAGAAGCACACACAGTGCT--G
* *
37498 AAACAGTAGGCACACACAGTGTTG
1 -AACAG-AAGCACACACAGTGCTG
* *
37522 AATAGAAGCACGCACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
37544 AACAGAGGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
37566 AACAGTAAGC
1 AACAG-AAGC
37576 GCGCTAGCGT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
22 38 0.60
23 7 0.11
24 6 0.10
25 7 0.11
26 5 0.08
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.13
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:39536 original size:16 final size:17
Alignment explanation
Indices: 39515--39547 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39505 TAAAAATTTT
39515 AAAAAAC-ACAAAAATA
1 AAAAAACTACAAAAATA
*
39531 AAAAAACTCCAAAAATA
1 AAAAAACTACAAAAATA
39548 TCAAAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (17 bp):
AAAAAACTACAAAAATA
Found at i:40639 original size:2 final size:2
Alignment explanation
Indices: 40632--40667 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40622 AAACACCTTA
40632 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40668 GGTTTATGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:73656 original size:59 final size:59
Alignment explanation
Indices: 73564--73682 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
73554 AAGACAATGC
*
73564 TGCAGACTTTTTCGACCATTTTAAAGTGGGGACCCCTTTTAGAAATTTTTAATTTTATA
1 TGCAGACTTTTTCGAACATTTTAAAGTGGGGACCCCTTTTAGAAATTTTTAATTTTATA
*
73623 TGCAGACTTTTTCGAACATTTTAAAGTGGGGACCCCTTTTAGGAATTTTTAATTTTATA
1 TGCAGACTTTTTCGAACATTTTAAAGTGGGGACCCCTTTTAGAAATTTTTAATTTTATA
73682 T
1 T
73683 TTATAGCTGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (59 bp):
TGCAGACTTTTTCGAACATTTTAAAGTGGGGACCCCTTTTAGAAATTTTTAATTTTATA
Found at i:110368 original size:59 final size:59
Alignment explanation
Indices: 110276--110396 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
110266 GTTTGTGGTT
*
110276 GTTGATTGAGCCTCAGCTCAGTTGACATCGTTGCAATTGCAACAATTCAAAGGACATAG
1 GTTGATTGAGCCTCAGCTCAATTGACATCGTTGCAATTGCAACAATTCAAAGGACATAG
* * *
110335 GTTGATTGAGCCTTAGCTCAATTGACATCGTTGCTATTGCAACAATTCAAAGGACGTAG
1 GTTGATTGAGCCTCAGCTCAATTGACATCGTTGCAATTGCAACAATTCAAAGGACATAG
110394 GTT
1 GTT
110397 TGAGCATGCT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (59 bp):
GTTGATTGAGCCTCAGCTCAATTGACATCGTTGCAATTGCAACAATTCAAAGGACATAG
Found at i:118332 original size:30 final size:30
Alignment explanation
Indices: 118298--118357 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
118288 TTAAGGCTTA
118298 ATTATTGA-TTTGG-ACTCTTAAAGTTTACTC
1 ATTATTGACTTTGGTA-TC-TAAAGTTTACTC
*
118328 ATTATTTACTTTGGTATCTAAAGTTTACTC
1 ATTATTGACTTTGGTATCTAAAGTTTACTC
118358 CTTACATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 19 0.70
31 7 0.26
32 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (30 bp):
ATTATTGACTTTGGTATCTAAAGTTTACTC
Found at i:118874 original size:20 final size:20
Alignment explanation
Indices: 118851--118889 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
118841 TTAAAATTCT
118851 TATAACATTTTCAATTTTTA
1 TATAACATTTTCAATTTTTA
** *
118871 TATATTATTTTGAATTTTT
1 TATAACATTTTCAATTTTT
118890 TAAATTAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TATAACATTTTCAATTTTTA
Found at i:118896 original size:19 final size:20
Alignment explanation
Indices: 118857--118896 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
118847 TTCTTATAAC
*
118857 ATTTTCAATTTTTATATATT
1 ATTTTCAATTTTTATAAATT
*
118877 ATTTTGAATTTTT-TAAATT
1 ATTTTCAATTTTTATAAATT
118896 A
1 A
118897 ATAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTTCAATTTTTATAAATT
Done.