Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004766.1 Kokia drynarioides strain JFW-HI SEQ_118369, 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: 32203
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Found at i:6278 original size:15 final size:16
Alignment explanation
Indices: 6258--6298 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
6248 CACATATCAT
6258 TTCCTTTCCTTAAC-C
1 TTCCTTTCCTTAACTC
**
6273 TTCC-TTCCTTTTCTC
1 TTCCTTTCCTTAACTC
6288 TTCCTTTCCTT
1 TTCCTTTCCTT
6299 TATTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCCTTTCCTTAACTC
Found at i:7664 original size:20 final size:21
Alignment explanation
Indices: 7626--7668 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
7616 CTAAAACTAC
* *
7626 TTTTACTGGTTTTATCTGGTT
1 TTTTACTGGTTTAAACTGGTT
7647 TTTTACTGG-TTAAACTGGTT
1 TTTTACTGGTTTAAACTGGTT
7667 TT
1 TT
7669 CTGCCAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.14, C:0.09, G:0.19, T:0.58
Consensus pattern (21 bp):
TTTTACTGGTTTAAACTGGTT
Found at i:17228 original size:28 final size:28
Alignment explanation
Indices: 17196--17275 Score: 142
Period size: 28 Copynumber: 2.9 Consensus size: 28
17186 TATTATAAAA
* *
17196 CATTCTAAGTAGTTTTTAAATATACCTT
1 CATTCGAAGTAGTTTTTAAATATACCGT
17224 CATTCGAAGTAGTTTTTAAATATACCGT
1 CATTCGAAGTAGTTTTTAAATATACCGT
17252 CATTCGAAGTAGTTTTTAAATATA
1 CATTCGAAGTAGTTTTTAAATATA
17276 ACTTTCTTAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (28 bp):
CATTCGAAGTAGTTTTTAAATATACCGT
Found at i:19535 original size:221 final size:220
Alignment explanation
Indices: 19144--19582 Score: 736
Period size: 221 Copynumber: 2.0 Consensus size: 220
19134 TAGTTCCTAA
* *
19144 AGAAGTTTATAGATATTAGAGATTAGCAAAATTTGATTGATTTGGCCACAAAATTCTCTTGGTTA
1 AGAAGTTTATAGATATTAGAGATTAGCAAAATTTGATTGATTTAGACACAAAATTCTCTTGGTTA
19209 TGATGAAAATCCCTTACGAGCTCAAACAGTTAACTACCATCATCCATTTTGTTGAAGTACTTCAT
66 TGATGAAAAT--CTTACGAGCTCAAACAGTTAACTACCATCATCCATTTTGTTGAAGTACTTCAT
* * *
19274 CAAACTTCTGATATGAAAGTTGAAGAAGTGCACTTACAAAAATCTCACCTGATGATAGGGCAAAA
129 CAAACTTCTGATATGAAAGTTGAAGAAGTGCACATACAAAAATCTCAACTGATGATA-GCCAAAA
19339 TAAAGTAAAAATATTTCCTTGACATTAG
193 TAAAGTAAAAATATTTCCTTGACATTAG
* * *
19367 AGAAGTTTATTGATATTAGAGGTTAGCAAAATTTTGATTGATTTAGACACAACATTCTCTTGGTT
1 AGAAGTTTATAGATATTAGAGATTAGCAAAA-TTTGATTGATTTAGACACAAAATTCTCTTGGTT
* * *
19432 ATGATGAATAT-TTACGAGCTCAAACAGTTAATTGCCATCATCCATTTTGTTGAAGTACTTCATC
65 ATGATGAAAATCTTACGAGCTCAAACAGTTAACTACCATCATCCATTTTGTTGAAGTACTTCATC
19496 AAACTTCTGATATGAAAGTTGAAGAAGTGCACATACAAAAATCTCAACTGATGATAGCCAAAATA
130 AAACTTCTGATATGAAAGTTGAAGAAGTGCACATACAAAAATCTCAACTGATGATAGCCAAAATA
19561 AAGTAAAAATATTTCCTTGACA
195 AAGTAAAAATATTTCCTTGACA
19583 ATCGAACATA
Statistics
Matches: 204, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
220 30 0.15
221 105 0.51
223 29 0.14
224 40 0.20
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (220 bp):
AGAAGTTTATAGATATTAGAGATTAGCAAAATTTGATTGATTTAGACACAAAATTCTCTTGGTTA
TGATGAAAATCTTACGAGCTCAAACAGTTAACTACCATCATCCATTTTGTTGAAGTACTTCATCA
AACTTCTGATATGAAAGTTGAAGAAGTGCACATACAAAAATCTCAACTGATGATAGCCAAAATAA
AGTAAAAATATTTCCTTGACATTAG
Found at i:26917 original size:59 final size:60
Alignment explanation
Indices: 26862--27072 Score: 246
Period size: 59 Copynumber: 3.5 Consensus size: 60
26852 AGAAGTTTGG
* * *
26862 GGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATATGATTTT-AAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGCTAAAATATGATTTTGAAAAAGTTTAA
* * * * * *
26921 GGGTTAACATGTAATTTGGGAAAAGTGTAGGGGGTAAAATATGATTTTTGGAAAAGTTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGCTAAAATATGA-TTTTGAAAAAGTTTAA
* * * * * * *
26982 GGTTTAAAATGTAATTTTAGAAAAGTTTAGGGGCCAAAATGTAATTTTGGAAAATTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGCTAAAATATGATTTTGAAAAAGTTTAA
*
27042 GGGTT-AAATGTAATTTTGGAAAATTTTAGGG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGG
27073 ATCTCTTGAG
Statistics
Matches: 128, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 62 0.48
60 22 0.17
61 44 0.34
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (60 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGCTAAAATATGATTTTGAAAAAGTTTAA
Found at i:26924 original size:29 final size:30
Alignment explanation
Indices: 26838--27069 Score: 200
Period size: 30 Copynumber: 7.8 Consensus size: 30
26828 ACACGGGATG
* * ** *
26838 AAAATA-AATTTTAGAGAAGTTTGGGGGTC
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
*
26867 AAAATATAATTTTGGAAAAGTTTAGGGGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
* *
26897 AAAATATGATTTT-AAAAAGTTTAAGGGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
* * * * * *
26926 AACATGTAATTTGGGAAAAGTGTAGGGGGT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
* * *
26956 AAAATATGATTTTTGGAAAAGTTTTAGGTTT
1 AAAATAT-AATTTTGGAAAAGTTTAAGGGTT
* * * **
26987 AAAATGTAATTTTAGAAAAGTTTAGGGGCC
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
* *
27017 AAAATGTAATTTTGGAAAATTTTAAGGGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
* *
27047 -AAATGTAATTTTGGAAAATTTTA
1 AAAATATAATTTTGGAAAAGTTTA
27070 GGGATCTCTT
Statistics
Matches: 163, Mismatches: 37, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
29 52 0.32
30 89 0.55
31 22 0.13
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (30 bp):
AAAATATAATTTTGGAAAAGTTTAAGGGTT
Found at i:28098 original size:10 final size:10
Alignment explanation
Indices: 28070--28104 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
28060 TTCAATGCTC
28070 TTTTTTGTAT
1 TTTTTTGTAT
*
28080 TGATTTTGTAT
1 T-TTTTTGTAT
28091 TTTTTTGTAT
1 TTTTTTGTAT
28101 TTTT
1 TTTT
28105 CATGGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.77
Consensus pattern (10 bp):
TTTTTTGTAT
Found at i:28898 original size:50 final size:50
Alignment explanation
Indices: 28843--29008 Score: 164
Period size: 50 Copynumber: 3.3 Consensus size: 50
28833 CTTTGTTCAA
28843 TCCACTG-ACACTTCAGGGATAAGAATTTTGGTGTTGAAGCTTCACTCCAT
1 TCCACTGCA-ACTTCAGGGATAAGAATTTTGGTGTTGAAGCTTCACTCCAT
* * * * * * *
28893 TCCACTGCAACTTCAAGGAGAT-TGAGA-TTCGCTATT-ATAGTCTTTA-TTCAA
1 TCCACTGCAACTTC-AGG-GATAAGA-ATTTTGGTGTTGA-AG-CTTCACTCCAT
28944 TCCACTG-ACACTTCAGGGATAAGAATTTTGGTGTTGAAGCTTCACTCCAT
1 TCCACTGCA-ACTTCAGGGATAAGAATTTTGGTGTTGAAGCTTCACTCCAT
28994 TCCACTGCAACTTCA
1 TCCACTGCAACTTCA
29009 TGGAGATTGA
Statistics
Matches: 90, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
49 8 0.09
50 43 0.48
51 31 0.34
52 8 0.09
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (50 bp):
TCCACTGCAACTTCAGGGATAAGAATTTTGGTGTTGAAGCTTCACTCCAT
Found at i:28921 original size:101 final size:101
Alignment explanation
Indices: 28782--29021 Score: 417
Period size: 101 Copynumber: 2.4 Consensus size: 101
28772 CTACTATAGT
* * * * *
28782 TTCACTTCATTTCACTACAACTTCAAGGAGATTAAGATTCGATATTATAGTCTTTGTTCAATCCA
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATTCGATATTATAGTCTTTATTCAATCCA
28847 CTGACACTTCAGGGATAAGAATTTTGGTGTTGAAGC
66 CTGACACTTCAGGGATAAGAATTTTGGTGTTGAAGC
*
28883 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATTCGCTATTATAGTCTTTATTCAATCCA
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATTCGATATTATAGTCTTTATTCAATCCA
28948 CTGACACTTCAGGGATAAGAATTTTGGTGTTGAAGC
66 CTGACACTTCAGGGATAAGAATTTTGGTGTTGAAGC
*
28984 TTCACTCCATTCCACTGCAACTTCATGGAGATTGAGAT
1 TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGAT
29022 CCGTTACTGT
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 132 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (101 bp):
TTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATTCGATATTATAGTCTTTATTCAATCCA
CTGACACTTCAGGGATAAGAATTTTGGTGTTGAAGC
Found at i:29324 original size:49 final size:49
Alignment explanation
Indices: 29271--29931 Score: 464
Period size: 49 Copynumber: 13.5 Consensus size: 49
29261 TGGAACGGGA
* *
29271 TTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* * * * * * * * *
29320 TTCGTCGTTACGACTTAAACCTTTCTCTCCAT-ATCCTTATGGTAC-TGG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGA-GGTACAAGG
** * * *
29368 ATTCATCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAAGTACAAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* * * * * * * *
29418 TTCGTCGTTGCGACTTAAACCTTTCGCTCCATATCTTC-GTGGTACTAGA
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCAT-GCTTCTGAGGTACAAGG
* * *
29467 TTCGCTGTTGC-AGCTTAAATATTTCCCTTCATGCTTCCGAGGTACAAGG
1 TTCGCCGTTGCGA-CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* * * * *
29516 TTCGCCGTTGCGACTTAAACCTTT-CCTTCCATATCTTC-GTGGTACTAGA
1 TTCGCCGTTGCGACTTAAATCTTTCCCTT-CAT-GCTTCTGAGGTACAAGG
* * * *
29565 TTCGCTGTTGCGGCTTAAATCTTTCCCTTTATGCTTCTGAGGTAAAAGG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* * * * * *
29614 TTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC-GTGGTACTAGA
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCAT-GCTTCTGAGGTACAAGG
* * *
29663 TTCGTCGTTAC-AGCTTAAATCTTTCCCTTTATGCTTCTGAGGTACAAGG
1 TTCGCCGTTGCGA-CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
** * * * * * * *
29712 TTCGCCGTTATGACTT-AAGCATTTCCCTCCATATCTT-AGTGGTACTAGA
1 TTCGCCGTTGCGACTTAAATC-TTTCCCTTCAT-GCTTCTGAGGTACAAGG
* * * ** *
29761 TTCGCCGTTGCGGCTTAAATCTTTCCTTTTATATTTCTGAGGTACAAGA
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* * * * *
29810 TTCGCCGTTGCGACTTAAA-CATTTCCCTCCATATCTTC-GTGGTACTAGA
1 TTCGCCGTTGCGACTTAAATC-TTTCCCTTCAT-GCTTCTGAGGTACAAGG
* * * * *
29859 TTCACCATTGCGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAAAG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
** * *
29908 TTCGTTGTTGTGACTTAAACCTTT
1 TTCGCCGTTGCGACTTAAATCTTT
29932 TCCTCCATAT
Statistics
Matches: 466, Mismatches: 122, Indels: 48
0.73 0.19 0.08
Matches are distributed among these distances:
48 34 0.07
49 398 0.85
50 34 0.07
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (49 bp):
TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
Found at i:29350 original size:98 final size:98
Alignment explanation
Indices: 29220--29951 Score: 986
Period size: 98 Copynumber: 7.5 Consensus size: 98
29210 TAAGGTGCTG
* * * **
29220 GGTTCGCCGTTGCGGTCGT-AACCTTTCCCTCCATATCTTCGTGGAACGGGATTCGTCGTTGCGG
1 GGTTCGCCGTTGC-GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGG
29284 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * * * *
29318 GGTTCGTCGTTACGACTTAAACCTTTCTCTCCATATCCTT-ATGGTACTGGATTCATCGTTGCGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATAT-CTTCGTGGTACTAGATTCGTCGTTGCGG
* *
29382 CTTAAATCTTTCCCTTCATGCTTCTAAAGTACAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * *
29416 GGTTCGTCGTTGCGACTTAAACCTTTCGCTCCATATCTTCGTGGTACTAGATTCG-CTGTTGCAG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTC-GTTGCGG
* *
29480 CTTAAATATTTCCCTTCATGCTTCCGAGGTACAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
*
29514 GGTTCGCCGTTGCGACTTAAACCTTTCCTTCCATATCTTCGTGGTACTAGATTCG-CTGTTGCGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTC-GTTGCGG
* *
29578 CTTAAATCTTTCCCTTTATGCTTCTGAGGTAAAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* *
29612 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTACAGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGC
*
29677 TTAAATCTTTCCCTTTATGCTTCTGAGGTACAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
** * * * *
29710 GGTTCGCCGTTATGACTTAAGCATTTCCCTCCATATCTTAGTGGTACTAGATTCGCCGTTGCGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGC
* * **
29775 TTAAATCTTTCCTTTTATATTTCTGAGGTACAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * ** *
29808 GATTCGCCGTTGCGACTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCACCATTGCGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGC
*
29873 TTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* ** * * *
29906 AGTTCGTTGTTGTGACTTAAACCTTTTCCTCCATATCTTCATGGTA
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
29952 ATGAAACCTG
Statistics
Matches: 565, Mismatches: 64, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
97 7 0.01
98 554 0.98
99 4 0.01
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (98 bp):
GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGCGGC
TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
Found at i:31717 original size:37 final size:37
Alignment explanation
Indices: 31658--31734 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
31648 AGCTTTTGAT
* *
31658 GAATTTGGCTCAGTGACGTCCATGTCCCACATAAAAA
1 GAATTTGGCTCAGTGACATCCATGCCCCACATAAAAA
*
31695 GAATTTGGCTC-GATGACATCCATGCCCCACGTAAAAA
1 GAATTTGGCTCAG-TGACATCCATGCCCCACATAAAAA
31732 GAA
1 GAA
31735 ACCATGATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 35 0.97
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (37 bp):
GAATTTGGCTCAGTGACATCCATGCCCCACATAAAAA
Found at i:31842 original size:15 final size:17
Alignment explanation
Indices: 31807--31842 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
31797 TTCATCGTGA
31807 CTTTCTTTTTCTTCCTT
1 CTTTCTTTTTCTTCCTT
31824 -TTTC-TTTTCTT-CTT
1 CTTTCTTTTTCTTCCTT
31838 CTTTC
1 CTTTC
31843 CCTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.17
15 11 0.61
16 4 0.22
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
CTTTCTTTTTCTTCCTT
Done.