Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010997.1 Kokia drynarioides strain JFW-HI SEQ_125967, 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: 6195
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:230 original size:96 final size:96
Alignment explanation
Indices: 56--237 Score: 217
Period size: 96 Copynumber: 1.9 Consensus size: 96
46 AAGGATATTT
** * * *
56 GATTATCTCGATTTGAAGAAAGGTTGCACATAGTAAGTTAAGATGCAATATTTCGGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACATAGTAAGTTAAGACGCAATATTTCGAAACCGAAGA
*
121 TAAGGAAACATTGCCTCGATTAAGGGTACTC
66 TAAAGAAACATTGCCTCGATTAAGGGTACTC
* * * *
152 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAACCCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACATAGTAAGTTAAGACGCAATA-TTTCGAAA-CCGAA
*
216 -ATGAAAG-AATATTGCCTCGATT
64 GAT-AAAGAAACATTGCCTCGATT
238 TAAAAGTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
95 1 0.01
96 64 0.89
97 7 0.10
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACATAGTAAGTTAAGACGCAATATTTCGAAACCGAAGA
TAAAGAAACATTGCCTCGATTAAGGGTACTC
Found at i:747 original size:30 final size:30
Alignment explanation
Indices: 712--979 Score: 281
Period size: 30 Copynumber: 8.9 Consensus size: 30
702 ACTCAGGATG
* * *
712 AAAATGAAATTTTAGAGAAGTTTGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
* * *
742 AAAATGTGATTTTGAAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
* * *
772 AAAATATGATTTTGGAAAAGTTTGAGGGATT
1 AAAATGTAATTTTGGAAAAGTTTGAGGG-TC
* *
803 AAAATGTAATTTTGGAAATGTTTGAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
* * * *
833 AAAATATGATTTTGGAGAAGTTTGAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
* * **
863 AAAATATAACTTTAAAAAAGTTT-AGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGA-GGGTC
*
893 AAAATGTAATTTTGGAAAAGTTT-AGGGGCC
1 AAAATGTAATTTTGGAAAAGTTTGA-GGGTC
*
923 AAAATGTAATTTTGGAAAAGTTTGAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTC
* *
953 AAAATGTAATTTTAGAAAAATTT-AGGG
1 AAAATGTAATTTTGGAAAAGTTTGAGGG
980 ACCTCTTGAG
Statistics
Matches: 203, Mismatches: 32, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
29 5 0.02
30 171 0.84
31 27 0.13
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTGAGGGTC
Found at i:937 original size:90 final size:90
Alignment explanation
Indices: 707--980 Score: 327
Period size: 91 Copynumber: 3.0 Consensus size: 90
697 AGAGAACTCA
* * * * * * *
707 GGATGAAAATGAAATTTTAGAGAAGTTTGAGGGTCAAAATGTGATTTTGAAAAAGTTTAAGGGTC
1 GGATCAAAATGTAATTTTGGAAAAGTTTGAGGGTCAAAATGTGATTTTGGAAAAGTTTGAGGGTT
* **
772 AAAATATGATTTTGGAAAAGTTTGAG
66 AAAATATAATTTTAAAAAAGTTT-AG
* * * * *
798 GGATTAAAATGTAATTTTGGAAATGTTTGAGGGTTAAAATATGATTTTGGAGAAGTTTGAGGGTT
1 GGATCAAAATGTAATTTTGGAAAAGTTTGAGGGTCAAAATGTGATTTTGGAAAAGTTTGAGGGTT
*
863 AAAATATAACTTTAAAAAAGTTTAG
66 AAAATATAATTTTAAAAAAGTTTAG
* * *
888 GGGTCAAAATGTAATTTTGGAAAAGTTT-AGGGGCCAAAATGTAATTTTGGAAAAGTTTGAGGGT
1 GGATCAAAATGTAATTTTGGAAAAGTTTGA-GGGTCAAAATGTGATTTTGGAAAAGTTTGAGGGT
*
952 TAAAATGTAATTTTAGAAAAA-TTTAG
65 TAAAATATAATTTTA-AAAAAGTTTAG
978 GGA
1 GGA
981 CCTCTTGAGC
Statistics
Matches: 155, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
89 1 0.01
90 76 0.49
91 78 0.50
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (90 bp):
GGATCAAAATGTAATTTTGGAAAAGTTTGAGGGTCAAAATGTGATTTTGGAAAAGTTTGAGGGTT
AAAATATAATTTTAAAAAAGTTTAG
Found at i:2693 original size:11 final size:10
Alignment explanation
Indices: 2676--2727 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
2666 ATAAGAATAT
2676 ATTTATTTTG
1 ATTTATTTTG
*
2686 AGTTTATTTAG
1 A-TTTATTTTG
* *
2697 ATACTATTTTT
1 AT-TTATTTTG
2708 ATTTATTTTG
1 ATTTATTTTG
2718 ATTTTATTTT
1 A-TTTATTTT
2728 TAATTTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.67
Consensus pattern (10 bp):
ATTTATTTTG
Found at i:2714 original size:21 final size:21
Alignment explanation
Indices: 2679--2735 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2669 AGAATATATT
*
2679 TATTTTGAGTTTATTTAGATAC
1 TATTTTTA-TTTATTTAGATAC
* **
2701 TATTTTTATTTATTTTGATTT
1 TATTTTTATTTATTTAGATAC
2722 TATTTTTAATTTAT
1 TATTTTT-ATTTAT
2736 AAAAAAGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (21 bp):
TATTTTTATTTATTTAGATAC
Found at i:3493 original size:26 final size:29
Alignment explanation
Indices: 3464--3517 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
3454 TTAAGGAACA
3464 AAATTGA-GG-TT-TTTAATTGATATTGG
1 AAATTGAGGGTTTATTTAATTGATATTGG
*
3490 AAATTTAGGGTTTATTTAATTGATATTG
1 AAATTGAGGGTTTATTTAATTGATATTG
3518 CTAATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
27 2 0.08
28 2 0.08
29 14 0.58
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.48
Consensus pattern (29 bp):
AAATTGAGGGTTTATTTAATTGATATTGG
Found at i:5877 original size:30 final size:29
Alignment explanation
Indices: 5836--6034 Score: 149
Period size: 29 Copynumber: 6.7 Consensus size: 29
5826 TACATGATAT
* * *
5836 AAATCCCATTTTTAATCTCGAAACCTTCAA
1 AAATTCCATTTTT-ACCCCGAAACCTTCAA
5866 AAATTCCATTTTTATCCCCG-AA-CTTCTAA
1 AAATTCCATTTTTA-CCCCGAAACCTTC-AA
*
5895 AAA-TCCTATTTTTTACCTCGAAACCTTCAA
1 AAATTCC-A-TTTTTACCCCGAAACCTTCAA
* * *
5925 AAATTTCATTTTTACCCCCAAACTTTCAA
1 AAATTCCATTTTTACCCCGAAACCTTCAA
* *
5954 AAA-TCTCATTTTTAACCCCAAAACTTTCAA
1 AAATTC-CATTTTT-ACCCCGAAACCTTCAA
* *
5984 AAATTCTAGTTTTACCCCCG-AA-CTTCTAA
1 AAATTCCATTTTTA-CCCCGAAACCTTC-AA
* *
6013 AAATCCCATTTTTGACCTCGAA
1 AAATTCCATTTTT-ACCCCGAA
6035 TTTTTCCAAA
Statistics
Matches: 137, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
28 11 0.08
29 60 0.44
30 58 0.42
31 8 0.06
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AAATTCCATTTTTACCCCGAAACCTTCAA
Found at i:5928 original size:59 final size:59
Alignment explanation
Indices: 5836--6034 Score: 265
Period size: 59 Copynumber: 3.4 Consensus size: 59
5826 TACATGATAT
* *
5836 AAATCCCATTTTTAATCTCGAAACCTTCAAAAATTCCATTTTTATCCCCGAACTTCTAA
1 AAATCCCATTTTTAACCTCGAAACCTTCAAAAATTCCATTTTTACCCCCGAACTTCTAA
* * * *
5895 AAATCCTATTTTTTACCTCGAAACCTTCAAAAATTTCATTTTTACCCCCAAACTT-TCAA
1 AAATCCCATTTTTAACCTCGAAACCTTCAAAAATTCCATTTTTACCCCCGAACTTCT-AA
* * * * * *
5954 AAATCTCATTTTTAACCCCAAAACTTTCAAAAATTCTAGTTTTACCCCCGAACTTCTAA
1 AAATCCCATTTTTAACCTCGAAACCTTCAAAAATTCCATTTTTACCCCCGAACTTCTAA
*
6013 AAATCCCATTTTTGACCTCGAA
1 AAATCCCATTTTTAACCTCGAA
6035 TTTTTCCAAA
Statistics
Matches: 118, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
58 1 0.01
59 116 0.98
60 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAATCCCATTTTTAACCTCGAAACCTTCAAAAATTCCATTTTTACCCCCGAACTTCTAA
Found at i:6060 original size:59 final size:58
Alignment explanation
Indices: 5836--6063 Score: 233
Period size: 59 Copynumber: 3.9 Consensus size: 58
5826 TACATGATAT
* * * * *
5836 AAATCCCATTTTTAATCTCGAAACCTTCAAAAATTCCATTTTTATCCCCGAACTTCTAA
1 AAATCCCATTTTTAACCTCGAAACTTTCAAAAATTTC-GTTTTACCCCCGAACTTCTAA
* * * * *
5895 AAATCCTATTTTTTACCTCGAAACCTTCAAAAATTTCATTTTTACCCCCAAACTT-TCAA
1 AAATCCCATTTTTAACCTCGAAACTTTCAAAAATTTC-GTTTTACCCCCGAACTTCT-AA
* * * *
5954 AAATCTCATTTTTAACCCCAAAACTTTCAAAAATTCTAGTTTTACCCCCGAACTTCTAA
1 AAATCCCATTTTTAACCTCGAAACTTTCAAAAATT-TCGTTTTACCCCCGAACTTCTAA
* ** * *
6013 AAATCCCATTTTTGACCTCGAATTTTTCCAAAATTATCGTTTCACCCCCGA
1 AAATCCCATTTTTAACCTCGAAACTTTCAAAAATT-TCGTTTTACCCCCGA
6064 GAATCCAAAA
Statistics
Matches: 141, Mismatches: 25, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
58 1 0.01
59 138 0.98
60 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.36
Consensus pattern (58 bp):
AAATCCCATTTTTAACCTCGAAACTTTCAAAAATTTCGTTTTACCCCCGAACTTCTAA
Found at i:6060 original size:118 final size:118
Alignment explanation
Indices: 5836--6061 Score: 292
Period size: 118 Copynumber: 1.9 Consensus size: 118
5826 TACATGATAT
* * * * *
5836 AAATCCCATTTTTAATCTCGAAACCTTCAAAAATTCCATTTTTATCCCCGAACTTCTAAAAATCC
1 AAATCCCATTTTTAACCCCAAAACCTTCAAAAATTCCAGTTTTACCCCCGAACTTCTAAAAATCC
* * * *
5901 TATTTTTTACCTCGAAACCTTCAAAAATTTCATTTTTACCCCCAAACTTTCAA
66 CATTTTTGACCTCGAAACCTTCAAAAATTTCAGTTTCACCCCCAAACTTTCAA
* * *
5954 AAATCTCATTTTTAACCCCAAAACTTTCAAAAATTCTAGTTTTACCCCCGAACTTCTAAAAATCC
1 AAATCCCATTTTTAACCCCAAAACCTTCAAAAATTCCAGTTTTACCCCCGAACTTCTAAAAATCC
*** *
6019 CATTTTTGACCTCGAATTTTTCCAAAATTATC-GTTTCACCCCC
66 CATTTTTGACCTCGAAACCTTCAAAAATT-TCAGTTTCACCCCC
6062 GAGAATCCAA
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
118 89 0.98
119 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.36
Consensus pattern (118 bp):
AAATCCCATTTTTAACCCCAAAACCTTCAAAAATTCCAGTTTTACCCCCGAACTTCTAAAAATCC
CATTTTTGACCTCGAAACCTTCAAAAATTTCAGTTTCACCCCCAAACTTTCAA
Done.