Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009090.1 Kokia drynarioides strain JFW-HI SEQ_123790, 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: 38880
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Found at i:319 original size:22 final size:22
Alignment explanation
Indices: 268--336 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
258 TGCACTAATG
* *
268 AACGGAGAGCACCAATGTGATA
1 AACGGAGAGCACAAATGTGCTA
*
290 TA-GAGAGAGCACAAATGTGCTA
1 AACG-GAGAGCACAAATGTGCTA
*
312 AACGGAGAGCACTAAACGTGCTA
1 AACGGAGAGCAC-AAATGTGCTA
335 AA
1 AA
337 TAACGAAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 26 0.67
23 12 0.31
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.14
Consensus pattern (22 bp):
AACGGAGAGCACAAATGTGCTA
Found at i:5792 original size:37 final size:37
Alignment explanation
Indices: 5743--5901 Score: 201
Period size: 37 Copynumber: 4.3 Consensus size: 37
5733 ACTCCGATAG
*
5743 AGAGCATAATGTTATATGGAAGGCTTGCATCTCGGTT
1 AGAGCATAATGTTATATGGAAGGCTTACATCTCGGTT
* *
5780 AGAGCATCATGTTATATGGAAGGCTTACGTCTCGGTT
1 AGAGCATAATGTTATATGGAAGGCTTACATCTCGGTT
** * *
5817 AGAGGGTAATGTTATATGGAAGACTTACATCTTGGTT
1 AGAGCATAATGTTATATGGAAGGCTTACATCTCGGTT
* * * * *
5854 ATAGCGTAATGTTATATGGAAGGCTTACGTTTGGGTT
1 AGAGCATAATGTTATATGGAAGGCTTACATCTCGGTT
*
5891 AAAGCATAATG
1 AGAGCATAATG
5902 CTATGTGACA
Statistics
Matches: 105, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.33
Consensus pattern (37 bp):
AGAGCATAATGTTATATGGAAGGCTTACATCTCGGTT
Found at i:9265 original size:52 final size:52
Alignment explanation
Indices: 9182--9362 Score: 247
Period size: 52 Copynumber: 3.5 Consensus size: 52
9172 AAAAAGGTTT
* * **
9182 GATGACTATGTGTCATCGTAAGTATACGAATCCTTTATAGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
9234 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATTG-GGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTA-TGAGGTCC
* * * *
9286 GATGACTATGTGTCATTGTGAGTATATGATTCCTTTACGGATTAAGAGATCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* * *
9338 AATAAATATGTGTCATCGTGAGTAT
1 GATGACTATGTGTCATCGTGAGTAT
9363 TAAATGAAAT
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
51 1 0.01
52 112 0.97
53 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
Found at i:14028 original size:52 final size:52
Alignment explanation
Indices: 13949--14133 Score: 275
Period size: 52 Copynumber: 3.6 Consensus size: 52
13939 TAAATGAAAA
* * *
13949 AGGTCTGATGAC--TGTGTCATCGCGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
13999 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
* * * *
14051 GGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACAGATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
* *
14103 AGGTCCGATGGCTATGTGTCATTGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
14134 TAAATGAATG
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
50 11 0.09
52 111 0.91
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
Found at i:14847 original size:21 final size:21
Alignment explanation
Indices: 14823--14870 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
14813 TAGAAGTAAG
** *
14823 ACTTGTTTCGGTAAAAGAGTC
1 ACTTGTTTCAATAAAACAGTC
*
14844 ACTTGTTTCAATAAAACTGTC
1 ACTTGTTTCAATAAAACAGTC
14865 ACTTGT
1 ACTTGT
14871 ATCGAAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
ACTTGTTTCAATAAAACAGTC
Found at i:16922 original size:36 final size:36
Alignment explanation
Indices: 16840--16922 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
16830 CACAATATAA
*
16840 TCACTATCACATGGCATGAAAAACATACCCACATAT
1 TCACTTTCACATGGCATGAAAAACATACCCACATAT
* ** * * *
16876 TTA-TTGTCACATGGTGTGAATAACATACCCTCATGT
1 TCACTT-TCACATGGCATGAAAAACATACCCACATAT
16912 TCACTTTCACA
1 TCACTTTCACA
16923 ATAGTCATCA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
35 1 0.03
36 34 0.92
37 2 0.05
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (36 bp):
TCACTTTCACATGGCATGAAAAACATACCCACATAT
Found at i:18606 original size:32 final size:33
Alignment explanation
Indices: 18570--18635 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
18560 ATTAGAAATA
18570 AGAAAGATAAATTCTA-TTACGATTTGAAAAGG
1 AGAAAGATAAATTCTAGTTACGATTTGAAAAGG
** * * *
18602 AGAAATTTGAATTCTAGTTAGGATTTTAAAAGG
1 AGAAAGATAAATTCTAGTTACGATTTGAAAAGG
18635 A
1 A
18636 TTAGTTTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (33 bp):
AGAAAGATAAATTCTAGTTACGATTTGAAAAGG
Found at i:20872 original size:21 final size:21
Alignment explanation
Indices: 20847--20890 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20837 TCCTATTGTC
*
20847 GTATTAGAGCTTTTACATGTT
1 GTATTAGAGATTTTACATGTT
**
20868 GTATTTTAGATTTTACATGTT
1 GTATTAGAGATTTTACATGTT
20889 GT
1 GT
20891 GATGCATGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.07, G:0.18, T:0.52
Consensus pattern (21 bp):
GTATTAGAGATTTTACATGTT
Found at i:30412 original size:51 final size:51
Alignment explanation
Indices: 30345--30573 Score: 325
Period size: 51 Copynumber: 4.5 Consensus size: 51
30335 AAAGGGTTCA
* *
30345 ATGACTAAGTCTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCAG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCG
*
30396 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCG
* * *
30447 ATTACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCG
* * * **
30498 ATGACTCAGTGTCATCGTGAGTATATGAATTCCTATATGGAACAAGAGGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTATGGATTAA-AGGTCCG
30551 ATGACTATA-TGTCATCGTGAGTA
1 ATGACTA-AGTGTCATCGTGAGTA
30574 TTAAATTAAA
Statistics
Matches: 159, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
51 121 0.76
52 10 0.06
53 27 0.17
54 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (51 bp):
ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCG
Found at i:31849 original size:56 final size:57
Alignment explanation
Indices: 31722--31875 Score: 195
Period size: 56 Copynumber: 2.7 Consensus size: 57
31712 TATATTATGA
* * *
31722 TTTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGTTATTAAATTATATACT
1 TTTTTATTAAATT-ATA-TTTAATAATAATCATATTAA-AATATGATTAAATTATATACT
* * * *
31781 ATTTTATTAAATTGTATTTAATAATAATCATGTTAAAATATGATTAAATTATTTA-T
1 TTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGATTAAATTATATACT
*
31837 TTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
1 TTTTTATTAAATTATATTTAATAATAATCATATTAAAAT
31876 TTAACAATAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
56 36 0.43
57 16 0.19
58 18 0.22
59 9 0.11
60 4 0.05
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (57 bp):
TTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGATTAAATTATATACT
Found at i:33785 original size:25 final size:25
Alignment explanation
Indices: 33757--33836 Score: 117
Period size: 25 Copynumber: 3.2 Consensus size: 25
33747 TTTCTCCTAG
*
33757 TTAAACATTGTTTTTAGTTTCTCAC
1 TTAAACTTTGTTTTTAGTTTCTCAC
*
33782 TTAAACTTTGTTTTTAGGTTCAT-AC
1 TTAAACTTTGTTTTTAGTTTC-TCAC
*
33807 TTAAACTTTATTTTTAGTTTCTCAC
1 TTAAACTTTGTTTTTAGTTTCTCAC
33832 TTAAA
1 TTAAA
33837 ACTCTGATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.02
25 47 0.96
26 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (25 bp):
TTAAACTTTGTTTTTAGTTTCTCAC
Done.