Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013487.1 Kokia drynarioides strain JFW-HI SEQ_128513, 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: 79015
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:5419 original size:20 final size:20
Alignment explanation
Indices: 5394--5434 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5384 AAAAGAAATA
*
5394 AGGCCCCTTCTATGAAGACC
1 AGGCCCCCTCTATGAAGACC
5414 AGGCCCCCTCTATGAAGACC
1 AGGCCCCCTCTATGAAGACC
5434 A
1 A
5435 TGGAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.37, G:0.20, T:0.17
Consensus pattern (20 bp):
AGGCCCCCTCTATGAAGACC
Found at i:6433 original size:28 final size:28
Alignment explanation
Indices: 6373--6444 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
6363 TTTGACCTCA
* * *
6373 AAACTTTCAAAAATTCGGATATGGCTCC
1 AAACTTTCCAAAATTTGGATATGGCCCC
**
6401 AAACTTTCCAAAATTTGGATATTTCCCC
1 AAACTTTCCAAAATTTGGATATGGCCCC
*
6429 CAACTTTCCAAAATTT
1 AAACTTTCCAAAATTT
6445 ACATTTTGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (28 bp):
AAACTTTCCAAAATTTGGATATGGCCCC
Found at i:6608 original size:30 final size:30
Alignment explanation
Indices: 6430--6784 Score: 147
Period size: 30 Copynumber: 11.9 Consensus size: 30
6420 TATTTCCCCC
* *
6430 AACTTTCCAAAATTTACATTTTGA-CCCCTA
1 AACTTTCCAAAAATCACA-TTTGACCCCCTA
* * * *
6460 ATCTTTCCAAAAATTAAATTTTGA-ACCC-A
1 AACTTTCCAAAAATCACA-TTTGACCCCCTA
* * * *
6489 AACTTTTCAAAAATCACATTTTAACCTC-A
1 AACTTTCCAAAAATCACATTTGACCCCCTA
*** ** *
6518 AA-TCTTCCAAAAATTTGGATTTGGTCCTC-A
1 AACT-TTCCAAAAA-TCACATTTGACCCCCTA
*** * *
6548 AACTTTCCGTGAATTACATTTTGA-CTCCTA
1 AACTTTCCAAAAATCACA-TTTGACCCCCTA
*
6578 AACTTTCCAAAAATCACATTTAACCCCCTA
1 AACTTTCCAAAAATCACATTTGACCCCCTA
* * ** *
6608 AAATTTTCAAAAATGCTGATTTGACCTCC-A
1 AACTTTCCAAAAAT-CACATTTGACCCCCTA
* *
6638 AACTTTCTAAAAATCACATTTTGACCTCC-A
1 AACTTTCCAAAAATCACA-TTTGACCCCCTA
* * * **
6668 TAGTTTCCAAAAATTCAAATTTGACTTCC-A
1 AACTTTCCAAAAA-TCACATTTGACCCCCTA
* * *
6698 AAGTTT-CAAAAATCACATTTTAGCCCCTA
1 AACTTTCCAAAAATCACATTTGACCCCCTA
* * * * * * *
6727 AACTTCCCAAATATCGCATTTTAACGCCTG
1 AACTTTCCAAAAATCACATTTGACCCCCTA
*
6757 AACTTTCCAAAAATTCATATTTGACCCC
1 AACTTTCCAAAAA-TCACATTTGACCCC
6785 TCGAACTCTC
Statistics
Matches: 244, Mismatches: 68, Indels: 25
0.72 0.20 0.07
Matches are distributed among these distances:
28 15 0.06
29 50 0.20
30 155 0.64
31 24 0.10
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (30 bp):
AACTTTCCAAAAATCACATTTGACCCCCTA
Found at i:6641 original size:60 final size:60
Alignment explanation
Indices: 6567--6737 Score: 168
Period size: 60 Copynumber: 2.9 Consensus size: 60
6557 TGAATTACAT
* **
6567 TTTGA-CTCCTAAACTTTCCAAAAATCACATTTAACCCCCTAAAATTTTCAAAAATGCTGA
1 TTTGACCTCC-AAACTTTCCAAAAATCACATTTAACCCCCTAAAATTTCCAAAAATGCAAA
* * * * * *
6627 TTTGACCTCCAAACTTTCTAAAAATCACATTTTGACCTCC-ATAGTTTCCAAAAATTCAAA
1 TTTGACCTCCAAACTTTCCAAAAATCACA-TTTAACCCCCTAAAATTTCCAAAAATGCAAA
* * * * * *
6687 TTTGACTTCCAAAGTTT-CAAAAATCACATTTTAGCCCCTAAACTTCCCAAA
1 TTTGACCTCCAAACTTTCCAAAAATCACATTTAACCCCCTAAAATTTCCAAA
6738 TATCGCATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
58 7 0.08
59 19 0.21
60 52 0.58
61 12 0.13
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (60 bp):
TTTGACCTCCAAACTTTCCAAAAATCACATTTAACCCCCTAAAATTTCCAAAAATGCAAA
Found at i:6825 original size:29 final size:28
Alignment explanation
Indices: 6757--6847 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 28
6747 TTAACGCCTG
* *
6757 AACTTTCCAAAAATTCATATTTGACCCCTCG
1 AACTTTCC-AAAATTCAT-TTTGA-CCTTCA
* *
6788 AACTCTCCAAAATTCGATTTAGACCTTCA
1 AACTTTCCAAAATTC-ATTTTGACCTTCA
6817 AACTTTCCAAAATTCAATTTTGACCTTCA
1 AACTTTCCAAAATTC-ATTTTGACCTTCA
6846 AA
1 AA
6848 AGCCCAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 32 0.62
30 11 0.21
31 9 0.17
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (28 bp):
AACTTTCCAAAATTCATTTTGACCTTCA
Found at i:15165 original size:31 final size:28
Alignment explanation
Indices: 15111--15214 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 28
15101 AATTAATGAG
15111 AATTTTCAAAATTAGTGGGTTTAATTAA
1 AATTTTCAAAATTAGTGGGTTTAATTAA
* *
15139 AATTTTCAAAACTTTGGTAGGGTTTAATTAG
1 AATTTTCAAAA--TTAGT-GGGTTTAATTAA
* * *
15170 GATTTGTCAAAAAATTAAG-GGATTTAAGTAA
1 AATTT-TC--AAAATT-AGTGGGTTTAATTAA
15201 AATTTTCTAAAATT
1 AATTTTC-AAAATT
15215 GTGAAGATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
28 11 0.18
29 6 0.10
30 6 0.10
31 28 0.47
32 4 0.07
33 1 0.02
34 4 0.07
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.40
Consensus pattern (28 bp):
AATTTTCAAAATTAGTGGGTTTAATTAA
Found at i:21107 original size:2 final size:2
Alignment explanation
Indices: 21100--21124 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21090 GTGGAATGAG
21100 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
21125 GGGGAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21414 original size:15 final size:15
Alignment explanation
Indices: 21394--21428 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21384 TTGGATTTAG
*
21394 TTTTTTTATGATATA
1 TTTTTTTATGAAATA
*
21409 TTTTTTTATTAAATA
1 TTTTTTTATGAAATA
21424 TTTTT
1 TTTTT
21429 AAATGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTTTTATGAAATA
Found at i:21447 original size:26 final size:25
Alignment explanation
Indices: 21409--21458 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
21399 TTATGATATA
*
21409 TTTTTTTATTAAATATTTTTAAATG
1 TTTTTTTAGTAAATATTTTTAAATG
*
21434 TTTTTTTGAGTAAATTTTTTTAAAT
1 TTTTTTT-AGTAAATATTTTTAAAT
21459 AACATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (25 bp):
TTTTTTTAGTAAATATTTTTAAATG
Found at i:28449 original size:29 final size:29
Alignment explanation
Indices: 28394--28450 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
28384 ATATTTATAT
* *
28394 ATAATTTTATAATTAAATTCCATTAAAAA
1 ATAATTTTATAATTAAATTCAAATAAAAA
*
28423 ATAATTTTATAATTAAATTTAAATAAAA
1 ATAATTTTATAATTAAATTCAAATAAAA
28451 TTACTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAATTTTATAATTAAATTCAAATAAAAA
Found at i:51290 original size:90 final size:85
Alignment explanation
Indices: 51132--51307 Score: 212
Period size: 90 Copynumber: 2.0 Consensus size: 85
51122 TGAGCTTTTT
* *
51132 GTGAAGATCAAGTGATCTGCATAGGAATTCGAAAAAAAAAAACAGTAAGTACATTATTAACAAGT
1 GTGAAGATCAAGTGATCTGCATAGGAATTCAAAAAAAAAAAACAGTAAGTACATTATCAACAAGT
*
51197 GAAGGACTACAGAATTGGGA
66 GAAGGACTACAAAATTGGGA
**
51217 GTGAAGATCAAGTGATCTGCATAAGG-ATTCCAACAACAAAAAAAAAACAGTAAGTGTATTATCA
1 GTGAAGATCAAGTGATCTGCAT-AGGAATT----CAA-AAAAAAAAAACAGTAAGTACATTATCA
* *
51281 ATGAA-TGAAGGACTATAAAATTGGGA
60 A-CAAGTGAAGGACTACAAAATTGGGA
51307 G
1 G
51308 ATTGAACCTA
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
85 25 0.32
86 3 0.04
89 2 0.03
90 45 0.58
91 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (85 bp):
GTGAAGATCAAGTGATCTGCATAGGAATTCAAAAAAAAAAAACAGTAAGTACATTATCAACAAGT
GAAGGACTACAAAATTGGGA
Found at i:63732 original size:9 final size:9
Alignment explanation
Indices: 63720--63751 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
63710 CGGAGGATTC
63720 GGTGGAGTT
1 GGTGGAGTT
*
63729 GGTGGAGTC
1 GGTGGAGTT
63738 GGTGGAGTT
1 GGTGGAGTT
63747 GGTGG
1 GGTGG
63752 TGCTGGTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.09, C:0.03, G:0.59, T:0.28
Consensus pattern (9 bp):
GGTGGAGTT
Found at i:63761 original size:12 final size:12
Alignment explanation
Indices: 63746--63787 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
63736 TCGGTGGAGT
63746 TGGTGGTGCTGG
1 TGGTGGTGCTGG
63758 TGGTGGTG-TAGG
1 TGGTGGTGCT-GG
* *
63770 CGGTGGCGCTGG
1 TGGTGGTGCTGG
63782 TGGTGG
1 TGGTGG
63788 AGTAGGAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.02, C:0.10, G:0.60, T:0.29
Consensus pattern (12 bp):
TGGTGGTGCTGG
Found at i:63774 original size:24 final size:24
Alignment explanation
Indices: 63747--63799 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
63737 CGGTGGAGTT
* * *
63747 GGTGGTGCTGGTGGTGGTGTAGGC
1 GGTGGCGCTGGTGGTGGAGTAGGA
63771 GGTGGCGCTGGTGGTGGAGTAGGA
1 GGTGGCGCTGGTGGTGGAGTAGGA
63795 GGTGG
1 GGTGG
63800 AGCCGGAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.08, C:0.08, G:0.60, T:0.25
Consensus pattern (24 bp):
GGTGGCGCTGGTGGTGGAGTAGGA
Found at i:69463 original size:16 final size:18
Alignment explanation
Indices: 69442--69474 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
69432 ACATTTAGTG
69442 AATATA-AATT-TTTTTA
1 AATATATAATTATTTTTA
69458 AATATATAATTATTTTT
1 AATATATAATTATTTTT
69475 TGAAACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATATATAATTATTTTTA
Found at i:72431 original size:19 final size:17
Alignment explanation
Indices: 72390--72432 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
72380 GAAAGAAAAT
72390 ATATTTTTATTTGGGCC
1 ATATTTTTATTTGGGCC
*
72407 ACATTTTTATTTTTGGGCC
1 ATATTTTTA--TTTGGGCC
*
72426 TTATTTT
1 ATATTTT
72433 ATGTCGAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (17 bp):
ATATTTTTATTTGGGCC
Found at i:72620 original size:44 final size:44
Alignment explanation
Indices: 72529--72625 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
72519 TTAGGTTCAC
* * * * **
72529 GCAAACGAAAGGGTGCAACTGTTGACCTGATGACTTGGGTTTAT
1 GCAAATGAAAGGGTGCAACCGTTGACCTGACGACCTAAGTTTAT
*
72573 GCAAATGAAAGGGTGCAACCGTTGACCCT-ACGACCTAAGTTTGT
1 GCAAATGAAAGGGTGCAACCGTTGA-CCTGACGACCTAAGTTTAT
72617 GCAATATGA
1 GCAA-ATGA
72626 GATGCTCGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
44 37 0.84
45 7 0.16
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.25
Consensus pattern (44 bp):
GCAAATGAAAGGGTGCAACCGTTGACCTGACGACCTAAGTTTAT
Done.