Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009692.1 Kokia drynarioides strain JFW-HI SEQ_124411, 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: 23698
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:66 original size:15 final size:15
Alignment explanation
Indices: 46--84 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
36 GCACATCAAA
*
46 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
61 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
75 CAAGAATTAA
1 CAAGAATTAA
85 ACACACTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:3201 original size:6 final size:6
Alignment explanation
Indices: 3187--3247 Score: 83
Period size: 6 Copynumber: 10.7 Consensus size: 6
3177 CCAGATTTCT
* *
3187 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTTAAA -TTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3232 TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
3248 TTTTCAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
5 13 0.27
6 35 0.73
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:3201 original size:17 final size:17
Alignment explanation
Indices: 3179--3247 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
3169 AATTTTGACC
*
3179 AGATTTCTTTTAAATTT
1 AGATTTATTTTAAATTT
3196 AGATTTATTTTAAATTT
1 AGATTTATTTTAAATTT
* **
3213 AAATTTAAATTAAATTT
1 AGATTTATTTTAAATTT
*
3230 A-ATTTAAATTTAAATTT
1 AGATTT-ATTTTAAATTT
3247 A
1 A
3248 TTTTCAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.09
17 42 0.91
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
AGATTTATTTTAAATTT
Found at i:5293 original size:30 final size:30
Alignment explanation
Indices: 5228--5688 Score: 375
Period size: 30 Copynumber: 15.7 Consensus size: 30
5218 GGAGTTCCCT
* * *
5228 AAACTATCC-AAAATTACAATTTTG-CCCCT
1 AAACT-TCCAAAAATTCCATTTTTGACCCCG
*
5257 AAACTTCAAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* * *
5287 AAACTTCAAAAAATTCCATTTTTGATCCTG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
5317 -AACTTCAAAAAATTCCATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
* *
5346 -AACTTCCAAAAATTCCAATTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
5375 AAACTTCCAAAAATTCCATTTTTGACCCACG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
*
5406 -AACTTCCAAAAATTCCA-TTTTGACCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* * *
5434 AAACTTCCAAAAATTCCATTTTTAACACCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* * * *
5464 AAATTTTCGAAAATTCCA-TTTTGACCCTTG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
* * **
5494 -AATTTCAAAAAATTCCATTTTCAACCCC-
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* *
5522 ATAACTTCCAAAAATTCCATTTTCGACCTCG
1 A-AACTTCCAAAAATTCCATTTTTGACCCCG
*
5553 AAACTTCC-AAAATTACA--TTTGAACCCTC-
1 AAACTTCCAAAAATTCCATTTTTG-ACCC-CG
* * **
5581 AAACCTCCAAAATTTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
5611 AAACTTTCAAAAATTACCA-TTTTG-CCCTCG
1 AAACTTCCAAAAATT-CCATTTTTGACCC-CG
* * * * *
5641 -AA-TGTCCAAAAACTCTATTTTCGACCTCA
1 AAACT-TCCAAAAATTCCATTTTTGACCCCG
*
5670 AAAC-TCCGAAAATTCCATT
1 AAACTTCCAAAAATTCCATT
5689 GTTACCCTCG
Statistics
Matches: 351, Mismatches: 55, Indels: 52
0.77 0.12 0.11
Matches are distributed among these distances:
27 3 0.01
28 19 0.05
29 156 0.44
30 163 0.46
31 10 0.03
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:5321 original size:59 final size:61
Alignment explanation
Indices: 5228--5700 Score: 359
Period size: 59 Copynumber: 8.0 Consensus size: 61
5218 GGAGTTCCCT
* * * *
5228 AAACTATCC-AAAATTACAATTTTGCCCCT-AAACTTCAAAAAATTCCATTTTTGACCC-CG
1 AAACT-TCCAAAAATTCCATTTTTGACCCTCGAACTTCAAAAAATTCCATTTTTGACCCTCG
* *
5287 AAACTTCAAAAAATTCCATTTTTGATCCT-GAACTTCAAAAAATTCCATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCTCGAACTTCAAAAAATTCCATTTTTGACCCTCG
* * *
5346 -AACTTCCAAAAATTCCAATTTTGA-CCTCGAAACTTCCAAAAATTCCATTTTTGACCCACG
1 AAACTTCCAAAAATTCCATTTTTGACCCTCG-AACTTCAAAAAATTCCATTTTTGACCCTCG
* * * * * *
5406 -AACTTCCAAAAATTCCA-TTTTGACCCCCAAACTTCCAAAAATTCCATTTTTAACAC-CA
1 AAACTTCCAAAAATTCCATTTTTGACCCTCGAACTTCAAAAAATTCCATTTTTGACCCTCG
* * * * * **
5464 AAATTTTCGAAAATTCCA-TTTTGACCCTTGAATTTCAAAAAATTCCATTTTCAACCC-C-
1 AAACTTCCAAAAATTCCATTTTTGACCCTCGAACTTCAAAAAATTCCATTTTTGACCCTCG
* * *
5522 ATAACTTCCAAAAATTCCATTTTCGA-CCTCGAAACTTC-CAAAATTACA--TTTGAACCCTC-
1 A-AACTTCCAAAAATTCCATTTTTGACCCTCG-AACTTCAAAAAATTCCATTTTTG-ACCCTCG
* * **
5581 AAACCTCCAAAATTTCCATTTTTGACCCTAAAACTTTC-AAAAATTACCA-TTTTG-CCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCTCGAAC-TTCAAAAAATT-CCATTTTTGACCCTCG
* * * * ** *
5641 -AA-TGTCCAAAAACTCTATTTTCGA-CCTCAAAAC-TCCGAAAATTCCATTGTT-ACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTGACCCTC-GAACTTCAAAAAATTCCATTTTTGACCCTCG
5699 AA
1 AA
5701 TATCTAAAAT
Statistics
Matches: 341, Mismatches: 50, Indels: 46
0.78 0.11 0.11
Matches are distributed among these distances:
57 10 0.03
58 77 0.23
59 212 0.62
60 38 0.11
61 4 0.01
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (61 bp):
AAACTTCCAAAAATTCCATTTTTGACCCTCGAACTTCAAAAAATTCCATTTTTGACCCTCG
Found at i:10340 original size:2 final size:2
Alignment explanation
Indices: 10333--10357 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10323 TAATTATACC
10333 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 A
10358 GATCATGAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12704 original size:25 final size:25
Alignment explanation
Indices: 12659--12715 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
12649 AAACAAACTG
*
12659 AAATAACAAAAATTAGCAAATAATAA
1 AAATAACAAAAAATA-CAAATAATAA
12685 AAATAACAAAATAATA-AAATAATAA
1 AAATAACAAAA-AATACAAATAATAA
*
12710 TAATAA
1 AAATAA
12716 GAATCAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 14 0.50
26 11 0.39
27 3 0.11
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (25 bp):
AAATAACAAAAAATACAAATAATAA
Found at i:12707 original size:8 final size:8
Alignment explanation
Indices: 12676--12715 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
12666 AAAAATTAGC
12676 AAATAATAA
1 AAATAAT-A
*
12685 AAATAACA
1 AAATAATA
12693 AAATAATA
1 AAATAATA
12701 AAATAATA
1 AAATAATA
12709 ATAATAA
1 A-AATAA
12716 GAATCAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 17 0.61
9 11 0.39
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (8 bp):
AAATAATA
Found at i:12777 original size:43 final size:44
Alignment explanation
Indices: 12692--12791 Score: 109
Period size: 46 Copynumber: 2.3 Consensus size: 44
12682 TAAAAATAAC
*
12692 AAAATAATAA-AATAATAATAATAAGAATCAAACCAGGGATAAACT
1 AAAATAATAATAATAATAATAATAAGAATCAAACCA--GATAAAAT
* *
12737 AAAATAATAATAATAATAATAATATGAAAT-AAACTA-ATAAAAT
1 AAAATAATAATAATAATAATAATAAG-AATCAAACCAGATAAAAT
*
12780 AAAGTAA-AATAA
1 AAAATAATAATAA
12792 ACAAGAAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
42 5 0.10
43 12 0.24
45 10 0.20
46 19 0.39
47 3 0.06
ACGTcount: A:0.66, C:0.05, G:0.06, T:0.23
Consensus pattern (44 bp):
AAAATAATAATAATAATAATAATAAGAATCAAACCAGATAAAAT
Found at i:19062 original size:13 final size:13
Alignment explanation
Indices: 19038--19082 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
19028 ATAAAAGGGA
19038 AAAAATTAAAATAT
1 AAAAATT-AAATAT
19052 AAAAATTAAATA-
1 AAAAATTAAATAT
19064 AAAAATGTAAATATT
1 AAAAAT-TAAATA-T
19079 AAAA
1 AAAA
19083 CAAAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.21
13 11 0.39
14 7 0.25
15 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
AAAAATTAAATAT
Found at i:19068 original size:20 final size:20
Alignment explanation
Indices: 19045--19096 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
19035 GGAAAAAATT
19045 AAAATATAAAAATTAAATA-A
1 AAAATATAAAAATTAAA-ACA
* *
19065 AAAATGTAAATATTAAAACA
1 AAAATATAAAAATTAAAACA
19085 AAAATA-AAAAAT
1 AAAATATAAAAAT
19097 GACTAAAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATATAAAAATTAAAACA
Found at i:19075 original size:26 final size:28
Alignment explanation
Indices: 19037--19097 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
19027 AATAAAAGGG
*
19037 AAAAAAT-TAAAATA-TAAAA-ATTAAAT
1 AAAAAATGTAAAATATTAAAACA-AAAAT
19063 AAAAAATGT-AAATATTAAAACAAAAAT
1 AAAAAATGTAAAATATTAAAACAAAAAT
19090 AAAAAATG
1 AAAAAATG
19098 ACTAAAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 12 0.39
27 18 0.58
28 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (28 bp):
AAAAAATGTAAAATATTAAAACAAAAAT
Found at i:22253 original size:18 final size:18
Alignment explanation
Indices: 22216--22266 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
22206 TATTTTTAGC
*
22216 AAAGAGAAGAATTTTTTTTT
1 AAAGAG-AG-ATTATTTTTT
22236 AAAGAGAGATTATTTTTT
1 AAAGAGAGATTATTTTTT
* *
22254 TACGAGAG-TTATT
1 AAAGAGAGATTATT
22267 ACTCATCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 5 0.18
18 15 0.54
19 2 0.07
20 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (18 bp):
AAAGAGAGATTATTTTTT
Found at i:22253 original size:19 final size:20
Alignment explanation
Indices: 22216--22255 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
22206 TATTTTTAGC
22216 AAAGAGAAGAATTTTTTTTT
1 AAAGAGAAGAATTTTTTTTT
22236 AAAGAG-AG-ATTATTTTTTT
1 AAAGAGAAGAATT-TTTTTTT
22255 A
1 A
22256 CGAGAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 10 0.53
20 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
AAAGAGAAGAATTTTTTTTT
Done.