Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010729.1 Kokia drynarioides strain JFW-HI SEQ_125682, 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: 14694
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Found at i:98 original size:3 final size:3
Alignment explanation
Indices: 41--84 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
31 TTAAACCCAT
41 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
85 ATGAATTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:754 original size:16 final size:16
Alignment explanation
Indices: 715--755 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
705 GGGTTCGGGC
715 GAATTTGGGCCATTTA
1 GAATTTGGGCCATTTA
*
731 G-GTTTGGGTCC-TTTA
1 GAATTTGGG-CCATTTA
746 GAATTTGGGC
1 GAATTTGGGC
756 TTAGGTTAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.17, C:0.12, G:0.32, T:0.39
Consensus pattern (16 bp):
GAATTTGGGCCATTTA
Found at i:847 original size:18 final size:18
Alignment explanation
Indices: 826--877 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
816 TTTTAATTAG
826 TTAAATTTTAAA-TTCAAA
1 TTAAATTTTAAACTT-AAA
*
844 TT-AATTTTAAACTTAAT
1 TTAAATTTTAAACTTAAA
861 TTAAA-TTTAAACTTAAA
1 TTAAATTTTAAACTTAAA
878 AGAAAAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 24 0.80
18 6 0.20
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAATTTTAAACTTAAA
Found at i:1693 original size:201 final size:201
Alignment explanation
Indices: 1346--1926 Score: 767
Period size: 201 Copynumber: 2.9 Consensus size: 201
1336 TGTGTTTCAT
* * * * * *
1346 CAGGAAGATGATTTTGGTTTACTTCCCCGTATTTCATCAAGAAGCTAACCGTTTTATTACTTCGA
1 CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCGTTTTATTACTTCGA
* * * * ** *
1411 CCTACTTCTAAGTATCTCATCAAGAAGTTGGGGTTAAAAAATTTGTTCATCGAGCGTGGGTTTGA
66 CCTGCTTCTAAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATCGAGCGTGGGTTTGA
* *
1476 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCATTTGTTTCAATCTGCTTCAC-
131 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCACT
1540 TCTCAA
196 TCTCAA
* * * * *
1546 CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCATGAAGCTAACC-ATTTGTTGCTTTGA
1 CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCGTTTTATTACTTCGA
* * *
1610 CCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGGGTGAGTTT
66 CCTGCTTCTAAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGTT--CATCGAGCGTGGGTTT
* * *
1675 GATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCGTTTGTTTCAATTTGCTTCT
129 GATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCA
*
1740 CTGTATCTCAT
194 C--T-TCTCAA
* * * *
1751 CAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGTTAACCGTTTTATTACTTCGA
1 CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCGTTTTATTACTTCGA
* *
1816 CCTGCTTCTCAGTGCCTCATCAGGAAGCTGGGGTTCGAAGATTTG-T--TCGAGCGTGGGTTTGA
66 CCTGCTTCTAAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATCGAGCGTGGGTTTGA
* *
1878 TTTGATCTTTTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGT
131 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGT
1927 GGATAATCGC
Statistics
Matches: 332, Mismatches: 42, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
199 49 0.15
200 43 0.13
201 135 0.41
205 52 0.16
206 53 0.16
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (201 bp):
CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCGTTTTATTACTTCGA
CCTGCTTCTAAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATCGAGCGTGGGTTTGA
TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCACT
TCTCAA
Found at i:13360 original size:96 final size:96
Alignment explanation
Indices: 13184--13364 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 96
13174 AGGATATTTG
* *
13184 ATTATTTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAAAT
1 ATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAAAATCGAAAAT
* *
13249 AAGGAAACATTGCCTCGATTAAGGGTATTCA
66 AAAGAAACATCGCCTCGATTAAGGGTATTCA
* * * *
13280 ATTATTTCTATTTGGAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTCAAAA-CTGGAA
1 ATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTCAAAATC-GAAA
*
13343 ATAAA-AGAATATCGCCTCGATT
64 ATAAAGA-AACATCGCCTCGATT
13365 TTAAAAGCTT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 3 0.04
96 70 0.96
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (96 bp):
ATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAAAATCGAAAAT
AAAGAAACATCGCCTCGATTAAGGGTATTCA
Found at i:13677 original size:31 final size:29
Alignment explanation
Indices: 13633--13704 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
13623 CCCGGGGGTG
*
13633 AAATGGTAATTTTAGGAAAATTTGAGGTTAA
1 AAATGGTAATTTTA-G-AAATTTGAGGCTAA
*
13664 AAATGG-AATTTTTAGACATTTGAGGCT-A
1 AAATGGTAA-TTTTAGAAATTTGAGGCTAA
*
13692 AAAGGGTAATTTT
1 AAATGGTAATTTT
13705 GAGAGTTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 10 0.28
29 12 0.33
30 3 0.08
31 11 0.31
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (29 bp):
AAATGGTAATTTTAGAAATTTGAGGCTAA
Found at i:13726 original size:58 final size:59
Alignment explanation
Indices: 13662--13794 Score: 153
Period size: 58 Copynumber: 2.3 Consensus size: 59
13652 ATTTGAGGTT
** *
13662 AAAAATGGAATTTTTAGACATTTGAGGCTAAAAGGGTAAT-TTT-GAGAGTTTTGAAGTC
1 AAAAATGGAATTTTTAGACATCCGAGGCTAAAAGGGTAATATTTGGA-AGTTTCGAAGTC
* * * * * * *
13720 GAAAATGGAGTTTTTGGACATCCGGGGGTAAAATGGTAATATTTGGAAGTTTCGAGGTC
1 AAAAATGGAATTTTTAGACATCCGAGGCTAAAAGGGTAATATTTGGAAGTTTCGAAGTC
13779 AAAAATGGAATTTTTA
1 AAAAATGGAATTTTTA
13795 AGGCCAAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
58 32 0.53
59 26 0.43
60 2 0.03
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGACATCCGAGGCTAAAAGGGTAATATTTGGAAGTTTCGAAGTC
Found at i:13793 original size:59 final size:57
Alignment explanation
Indices: 13602--13793 Score: 174
Period size: 59 Copynumber: 3.3 Consensus size: 57
13592 TACTTGGGGG
* * *
13602 CAAAAATGGTAA-TTTTGGA-TTCCCGGGGGTGAAATGGTAATTTTAGGAAAATTTGAGGT
1 CAAAAATGG-AATTTTTGGACAT-CCGGGGGTAAAATGGTAATTTT-GG-AAGTTTGAGGT
* * ** * * * *
13661 TAAAAATGGAATTTTTAGACATTTGAGGCTAAAAGGGTAATTTT-GAGAGTTTTGAAGT
1 CAAAAATGGAATTTTTGGACATCCGGGGGTAAAATGGTAATTTTGGA-AG-TTTGAGGT
* *
13719 CGAAAATGGAGTTTTTGGACATCCGGGGGTAAAATGGTAATATTTGGAAGTTTCGAGGT
1 CAAAAATGGAATTTTTGGACATCCGGGGGTAAAATGGTAAT-TTTGGAAGTTT-GAGGT
13778 CAAAAATGGAATTTTT
1 CAAAAATGGAATTTTT
13794 AAGGCCAAAA
Statistics
Matches: 103, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
56 1 0.01
57 2 0.02
58 44 0.43
59 53 0.51
60 3 0.03
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (57 bp):
CAAAAATGGAATTTTTGGACATCCGGGGGTAAAATGGTAATTTTGGAAGTTTGAGGT
Found at i:13903 original size:59 final size:58
Alignment explanation
Indices: 13829--14169 Score: 312
Period size: 59 Copynumber: 5.8 Consensus size: 58
13819 GTTCGACGGT
* * *
13829 AAAAATGGGATTTTTTGAAAGTTCGAGGGTAAAAATGGAATTTATGAAAGTTTTGGGGTT
1 AAAAATGGGA-TTTTTGGAAGTTCGAGGGTAAAAATGGAATTT-TTAAAGTTTTGGGGTC
* * * * *
13889 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAAGGTATTTTTTTAAGTTTTAGGGT-
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG-AATTTTTAAAGTTTTGGGGTC
** * * * * *
13947 AAAAATGTTATTTTTTGAAGTTTG-GGTGTAAAAATGAAATTTTTAGAAGTTTCGAGGTC
1 AAAAATGGGATTTTTGGAAGTTCGAGG-GTAAAAATGGAATTTTTA-AAGTTTTGGGGTC
* * **
14006 AAAAATGAGATTTTTGGAAGTAT-GGGGTGTAAAAATAAAATTTTTAAAAGTTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGT-TCGAGG-GTAAAAATGGAATTTTT-AAAGTTTTGGGGTC
* ** * * *
14066 AAAAATAGGATTTTTGGAAGTTTAAGGGTAAAATTTGAATTTTTAGAAGTTTTAGGGTC
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTA-AAGTTTTGGGGTC
* *
14125 AAAAATGGGATTTTTGGAAGTAC-AGGGGTAAAAAATAGAATTTTT
1 AAAAATGGGATTTTTGGAAGTTCGA-GGGT-AAAAATGGAATTTTT
14170 GGATAGTTTA
Statistics
Matches: 233, Mismatches: 37, Indels: 22
0.80 0.13 0.08
Matches are distributed among these distances:
57 8 0.03
58 39 0.17
59 106 0.45
60 79 0.34
61 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.37
Consensus pattern (58 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAAAGTTTTGGGGTC
Found at i:14159 original size:30 final size:29
Alignment explanation
Indices: 13808--14179 Score: 227
Period size: 30 Copynumber: 12.6 Consensus size: 29
13798 CCAAAAATCA
* *
13808 AATTTTTGGAAG-TTCGACGGTAAAAATGGG
1 AATTTTTGGAAGTTTAG-GGGTAAAAAT-GG
* * *
13838 ATTTTTTGAAAG-TTCGAGGGTAAAAATGG
1 AATTTTTGGAAGTTTAG-GGGTAAAAATGG
* * *
13867 AATTTATGAAAGTTTTGGGGTTAAAAATGG
1 AATTTTTGGAAGTTTAGGGG-TAAAAATGG
* ** *
13897 GATTTTTGGAAGTTCGGGGGTAAAAAAGG
1 AATTTTTGGAAGTTTAGGGGTAAAAATGG
* ** *
13926 TATTTTTTTAAGTTTTA-GGGTAAAAATGT
1 AATTTTTGGAAG-TTTAGGGGTAAAAATGG
* * *
13955 TATTTTTTGAAGTTT-GGGTGTAAAAATGA
1 AATTTTTGGAAGTTTAGGG-GTAAAAATGG
* * *
13984 AATTTTTAGAAGTTTCGAGGTCAAAAAT-G
1 AATTTTTGGAAGTTTAGGGGT-AAAAATGG
* * **
14013 AGATTTTTGGAAGTATGGGGTGTAAAAATAA
1 A-ATTTTTGGAAGTTTAGGG-GTAAAAATGG
** *
14044 AATTTTTAAAAGTTTTGGGGTCAAAAATAGG
1 AATTTTTGGAAGTTTAGGGGT-AAAAAT-GG
* * *
14075 -ATTTTTGGAAGTTTAAGGGTAAAATTTG
1 AATTTTTGGAAGTTTAGGGGTAAAAATGG
*
14103 AATTTTTAGAAGTTTTA-GGGTCAAAAATGG
1 AATTTTTGGAAG-TTTAGGGGT-AAAAATGG
* ** *
14133 GATTTTTGGAAGTACAGGGGTAAAAAATAG
1 AATTTTTGGAAGTTTAGGGGT-AAAAATGG
14163 AATTTTTGGATAGTTTA
1 AATTTTTGGA-AGTTTA
14180 AGGACCTCCA
Statistics
Matches: 271, Mismatches: 54, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
28 6 0.02
29 101 0.37
30 157 0.58
31 7 0.03
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (29 bp):
AATTTTTGGAAGTTTAGGGGTAAAAATGG
Done.