Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012895.1 Kokia drynarioides strain JFW-HI SEQ_127909, 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: 37218
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:578 original size:40 final size:40
Alignment explanation
Indices: 493--816 Score: 352
Period size: 40 Copynumber: 8.2 Consensus size: 40
483 TATAGCTTTA
* * * ** * *
493 GGGGTAAAAGATTTGATGGTCTTTAATCTGCTTTTTTATT
1 GGGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGATT
* * *
533 AGGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGGTC
1 GGGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGATT
* * * *
573 GGGGTAAAAGATTGGATTG-CTTCAGTCTGCCCTATGATC
1 GGGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGATT
*
612 GGGGTAAAAGATTGGTTGGTCTTCAATTTG-CCTCATGATT
1 GGGGTAAAAGATTGGATGGTCTTCAATTTGCCCT-ATGATT
* * * *
652 GGGGTAAAAAGATTGGATTG-CTTCAATTTGCCCCATCATC
1 GGGGT-AAAAGATTGGATGGTCTTCAATTTGCCCTATGATT
* * *
692 GGGGTAAAAGATTGGATAG-CTTCAATTTGCCCCATGGTT
1 GGGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGATT
* *
731 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTTTGATT
1 GGGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGATT
* * *
771 AGGGTAAAAGATTGGATGGTCTTCAATCTGCCC-ATGGTT
1 GGGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGATT
810 GGGGTAA
1 GGGGTAA
817 GAGGTTAGAT
Statistics
Matches: 241, Mismatches: 38, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
39 95 0.39
40 132 0.55
41 14 0.06
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (40 bp):
GGGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGATT
Found at i:620 original size:79 final size:79
Alignment explanation
Indices: 534--816 Score: 392
Period size: 79 Copynumber: 3.6 Consensus size: 79
524 TTTTTTATTA
* *
534 GGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGGTCGGGGTAAAAGATTGGATTGCTTCAGT
1 GGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGGTTGGGGTAAAAGATTGGATTGCTTCAAT
599 CTGCCCTATGATCG
66 CTGCCCTATGATCG
* *
613 GGGTAAAAGATTGGTTGGTCTTCAATTTG-CCTCATGATTGGGGTAAAAAGATTGGATTGCTTCA
1 GGGTAAAAGATTGGATGGTCTTCAATTTGCCCT-ATGGTTGGGGT-AAAAGATTGGATTGCTTCA
* * *
677 ATTTGCCCCATCATCG
64 ATCTGCCCTATGATCG
* * *
693 GGGTAAAAGATTGGATAG-CTTCAATTTGCCCCATGGTTGGGGTAAAAGATTGGATGGTCTTCAA
1 GGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGGTTGGGGTAAAAGATTGGATTG-CTTCAA
* **
757 TCTGCCCTTTGATTA
65 TCTGCCCTATGATCG
*
772 GGGTAAAAGATTGGATGGTCTTCAATCTGCCC-ATGGTTGGGGTAA
1 GGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGGTTGGGGTAA
817 GAGGTTAGAT
Statistics
Matches: 179, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
78 16 0.09
79 102 0.57
80 61 0.34
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (79 bp):
GGGTAAAAGATTGGATGGTCTTCAATTTGCCCTATGGTTGGGGTAAAAGATTGGATTGCTTCAAT
CTGCCCTATGATCG
Found at i:704 original size:119 final size:119
Alignment explanation
Indices: 493--803 Score: 410
Period size: 119 Copynumber: 2.6 Consensus size: 119
483 TATAGCTTTA
* * * * *
493 GGGGTAAAAGATTTGATGGTCTTTAATCTGCTTTTTTATTAGGGTAAAAGATTGGATGGTCTTCA
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCTCTTGATTAGGGTAAAAGATTGGATGGTCTTCA
* ** * * *
558 ATTTGCCCTATGGTCGGGGTAAAAGATTGGATTGCTTCAGTCTGCCCTATGATC
66 ATTTGCCCCATCATCGGGGTAAAAGATTGGATAGCTTCAATCTGCCCCATGATC
* * * * *
612 GGGGTAAAAGATTGGTTGGTCTTCAATTTGCCTCATGATTGGGGTAAAAAGATTGGATTG-CTTC
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCTCTTGATTAGGGT-AAAAGATTGGATGGTCTTC
* * *
676 AATTTGCCCCATCATCGGGGTAAAAGATTGGATAGCTTCAATTTGCCCCATGGTT
65 AATTTGCCCCATCATCGGGGTAAAAGATTGGATAGCTTCAATCTGCCCCATGATC
731 GGGGTAAAAGATTGGATGGTCTTCAATCTGCC-CTTTGATTAGGGTAAAAGATTGGATGGTCTTC
1 GGGGTAAAAGATTGGATGGTCTTCAATCTGCCTC-TTGATTAGGGTAAAAGATTGGATGGTCTTC
*
795 AATCTGCCC
65 AATTTGCCC
804 ATGGTTGGGG
Statistics
Matches: 164, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
118 14 0.09
119 137 0.84
120 13 0.08
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.34
Consensus pattern (119 bp):
GGGGTAAAAGATTGGATGGTCTTCAATCTGCCTCTTGATTAGGGTAAAAGATTGGATGGTCTTCA
ATTTGCCCCATCATCGGGGTAAAAGATTGGATAGCTTCAATCTGCCCCATGATC
Found at i:1051 original size:50 final size:50
Alignment explanation
Indices: 932--1166 Score: 175
Period size: 50 Copynumber: 4.7 Consensus size: 50
922 TACGATTTTT
* * * * * * *
932 AATCCGCCCCTCCACAACTTGAGGGGTATAAGATTTGCTCTTGTAGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTCGCTCTTGCAGCTTC
* * * * * * *
982 AATTTACCCTTTTTCAGCTTCAGGAGTATAAGATTCGCTCTTGCAGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTCGCTCTTGCAGCTTC
* * * * *
1032 AATCTGCCCCTCTAGAGCTTTAGGTGAATGAGATTCGC-CATTGCGGCTTT
1 AATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTCGCTC-TTGCAGCTTC
* * * * * * *
1082 AATCTGCCCCTCTATAGTTTTAGGTGTATGAGATTTGTTATTGCGGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTCGCTCTTGCAGCTTC
** * * *
1132 AATCTGTTCCTCTACGGCTTTAGGGGTATAGGATT
1 AATCTGCCCCTCTACAGCTTTAGGTGTATAAGATT
1167 TGATGTTCTA
Statistics
Matches: 144, Mismatches: 39, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
49 1 0.01
50 143 0.99
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (50 bp):
AATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTCGCTCTTGCAGCTTC
Found at i:12813 original size:30 final size:30
Alignment explanation
Indices: 12767--12942 Score: 203
Period size: 30 Copynumber: 5.9 Consensus size: 30
12757 TTAAAATCGA
* *
12767 GTCATATTTAAATTTTTGGAAAGTTCAAGG
1 GTCAAATTTGAATTTTTGGAAAGTTCAAGG
* *
12797 GTCAAATTGGAATTTTTGAAAAGATT-AAGG
1 GTCAAATTTGAATTTTTGGAAAG-TTCAAGG
* * **
12827 GTTAAATTTGATTTTTTGGAAA-TTTTAGG
1 GTCAAATTTGAATTTTTGGAAAGTTCAAGG
*
12856 GTTCAAATTTGAATTTTTGGAAAGTTTAAGG
1 G-TCAAATTTGAATTTTTGGAAAGTTCAAGG
* ** *
12887 GTCAAATTTAAATTTTTAAAAAGTTCAGGG
1 GTCAAATTTGAATTTTTGGAAAGTTCAAGG
12917 GTCAAATTTGAATTTTTGGAAAGTTC
1 GTCAAATTTGAATTTTTGGAAAGTTC
12943 GTGTGTCAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
28 2 0.02
29 4 0.03
30 107 0.88
31 9 0.07
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (30 bp):
GTCAAATTTGAATTTTTGGAAAGTTCAAGG
Found at i:12924 original size:90 final size:90
Alignment explanation
Indices: 12772--12938 Score: 246
Period size: 90 Copynumber: 1.9 Consensus size: 90
12762 ATCGAGTCAT
* * *
12772 ATTTAAATTTTTGGAAAGTTCAAGGGTCAAATTGGAATTTTTGAAAAGATTAAGGGTTAAATTTG
1 ATTTAAATTTTTGGAAAGTTCAAGGGTCAAATTGAAATTTTTAAAAAGATTAAGGGTCAAATTTG
*
12837 ATTTTTTGGAAATTTTAGGGTTCAA
66 AATTTTTGGAAATTTTAGGGTTCAA
* * * *
12862 ATTTGAATTTTTGGAAAGTTTAAGGGTCAAATTTAAATTTTTAAAAAG-TTCAGGGGTCAAATTT
1 ATTTAAATTTTTGGAAAGTTCAAGGGTCAAATTGAAATTTTTAAAAAGATT-AAGGGTCAAATTT
12926 GAATTTTTGGAAA
65 GAATTTTTGGAAA
12939 GTTCGTGTGT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
89 2 0.03
90 66 0.97
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (90 bp):
ATTTAAATTTTTGGAAAGTTCAAGGGTCAAATTGAAATTTTTAAAAAGATTAAGGGTCAAATTTG
AATTTTTGGAAATTTTAGGGTTCAA
Found at i:12940 original size:60 final size:60
Alignment explanation
Indices: 12767--12941 Score: 233
Period size: 60 Copynumber: 2.9 Consensus size: 60
12757 TTAAAATCGA
* * * * *
12767 GTCATATTTAAATTTTTGGAAAGTTCAAGGGTCAAATTGGAATTTTTGAAAAGATTAAGG
1 GTCAAATTTAAATTTTTGGAAAGTTCAGGGGTCAAATTTGAATTTTTGGAAAGTTTAAGG
* * * * * *
12827 GTTAAATTTGATTTTTTGGAAATTTTAGGGTTCAAATTTGAATTTTTGGAAAGTTTAAGG
1 GTCAAATTTAAATTTTTGGAAAGTTCAGGGGTCAAATTTGAATTTTTGGAAAGTTTAAGG
**
12887 GTCAAATTTAAATTTTTAAAAAGTTCAGGGGTCAAATTTGAATTTTTGGAAAGTT
1 GTCAAATTTAAATTTTTGGAAAGTTCAGGGGTCAAATTTGAATTTTTGGAAAGTT
12942 CGTGTGTCAA
Statistics
Matches: 96, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (60 bp):
GTCAAATTTAAATTTTTGGAAAGTTCAGGGGTCAAATTTGAATTTTTGGAAAGTTTAAGG
Found at i:12952 original size:90 final size:91
Alignment explanation
Indices: 12767--12952 Score: 234
Period size: 90 Copynumber: 2.1 Consensus size: 91
12757 TTAAAATCGA
* * * *
12767 GTCATATTTAAATTTTTGGAAAGTTCAAGGGTCAAATTGGAATTTTTGAAAAGATTAAGGGTTAA
1 GTCAAATTTAAATTTTTGGAAAGTTCAAGGGTCAAATTGAAATTTTTAAAAAGATTAAGGGTCAA
* *
12832 ATTTGATTTTTTGGAAATTTTAGGGT
66 ATTTGAATTTTTGGAAATGTTAGGGT
* * * *
12858 -TCAAATTTGAATTTTTGGAAAGTTTAAGGGTCAAATTTAAATTTTTAAAAAG-TTCAGGGGTCA
1 GTCAAATTTAAATTTTTGGAAAGTTCAAGGGTCAAATTGAAATTTTTAAAAAGATT-AAGGGTCA
* *
12921 AATTTGAATTTTTGGAAA-GTTCGTGT
65 AATTTGAATTTTTGGAAATGTTAGGGT
12947 GTCAAA
1 GTCAAA
12953 ACATAATTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
89 7 0.09
90 74 0.91
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (91 bp):
GTCAAATTTAAATTTTTGGAAAGTTCAAGGGTCAAATTGAAATTTTTAAAAAGATTAAGGGTCAA
ATTTGAATTTTTGGAAATGTTAGGGT
Found at i:13731 original size:63 final size:59
Alignment explanation
Indices: 13627--13799 Score: 196
Period size: 55 Copynumber: 2.9 Consensus size: 59
13617 GTAATTTGGG
*
13627 TTTTTTATTTATTTATTTATATTCA-AAAAGTAATAAATAAATAATAAAACAAAATTAATATAA
1 TTTTATATTTATTTATTTATATTCATAAAA-TAATAAATAAATAATAAAA-AAAA-T-AT-TAA
* * * *
13690 TTTTATATTTATTTATTTATATTCATACAATAATAAATAAAT--T-TAAATAATATTTA
1 TTTTATATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAAAAAATATTAA
*
13746 -TTTATATTTATTTATTTATATTCATAAAATAATAAAT-AATAAATAAATAAAATA
1 TTTTATATTTATTTATTTATATTCATAAAATAATAAATAAAT-AATAAAAAAAATA
13800 AAATAAAAAA
Statistics
Matches: 96, Mismatches: 9, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
54 3 0.03
55 36 0.38
56 2 0.02
57 3 0.03
58 7 0.07
59 3 0.03
60 2 0.02
61 1 0.01
63 36 0.38
64 3 0.03
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (59 bp):
TTTTATATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAAAAAATATTAA
Found at i:13757 original size:14 final size:14
Alignment explanation
Indices: 13740--13767 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13730 ATTTAAATAA
13740 TATTTATTTATATT
1 TATTTATTTATATT
13754 TATTTATTTATATT
1 TATTTATTTATATT
13768 CATAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTATTTATATT
Found at i:13810 original size:28 final size:27
Alignment explanation
Indices: 13769--13821 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
13759 ATTTATATTC
* *
13769 ATAAAATAATAAATAATAAATAAATAAA
1 ATAAAATAAAAAATAAGAAA-AAATAAA
13797 ATAAAATAAAAAATAAGAAAAAATA
1 ATAAAATAAAAAATAAGAAAAAATA
13822 GAATTGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (27 bp):
ATAAAATAAAAAATAAGAAAAAATAAA
Found at i:13812 original size:17 final size:18
Alignment explanation
Indices: 13772--13821 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
13762 TATATTCATA
* *
13772 AAATAATAAATAATAAAT
1 AAATAAGAAAAAATAAAT
13790 AAATAA-AATAAAATAAA-
1 AAATAAGAA-AAAATAAAT
13807 AAATAAGAAAAAATA
1 AAATAAGAAAAAATA
13822 GAATTGGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATAAGAAAAAATAAAT
Found at i:25339 original size:19 final size:18
Alignment explanation
Indices: 25300--25339 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
25290 TATAATTAAT
*
25300 TAAAAGGCAAAAAATATG
1 TAAAAGGCAAAAAATAAG
*
25318 TAAAAGGCATACAAATAAG
1 TAAAAGGCA-AAAAATAAG
25337 TAA
1 TAA
25340 CAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.60, C:0.07, G:0.15, T:0.17
Consensus pattern (18 bp):
TAAAAGGCAAAAAATAAG
Found at i:25428 original size:24 final size:24
Alignment explanation
Indices: 25401--25451 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
25391 ACTAGCATAA
*
25401 AAATAACAAATAAAT-AAATTACAT
1 AAATAA-AAATAAATAAAATTAAAT
*
25425 AAATAATAATAAATAAAATTAAAT
1 AAATAAAAATAAATAAAATTAAAT
25449 AAA
1 AAA
25452 AGCAAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (24 bp):
AAATAAAAATAAATAAAATTAAAT
Found at i:25500 original size:17 final size:16
Alignment explanation
Indices: 25462--25515 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
25452 AGCAAGAATG
*
25462 TAAATAACAAAGAAAA
1 TAAATAACAAAAAAAA
*
25478 TGAATAACAAATAAAAA
1 TAAATAACAAA-AAAAA
* *
25495 TAAATAA-ATAAAAAT
1 TAAATAACAAAAAAAA
25510 TAAATA
1 TAAATA
25516 CTATATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 10 0.31
16 12 0.38
17 10 0.31
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (16 bp):
TAAATAACAAAAAAAA
Found at i:25505 original size:14 final size:15
Alignment explanation
Indices: 25486--25515 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
25476 AATGAATAAC
25486 AAATAAAAA-TAAAT
1 AAATAAAAATTAAAT
25500 AAATAAAAATTAAAT
1 AAATAAAAATTAAAT
25515 A
1 A
25516 CTATATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAATTAAAT
Found at i:26177 original size:16 final size:16
Alignment explanation
Indices: 26156--26186 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26146 TGGAGGTAAC
26156 AAAAAAACCCTTTTTA
1 AAAAAAACCCTTTTTA
*
26172 AAAAAAACTCTTTTT
1 AAAAAAACCCTTTTT
26187 CACAACCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAAAACCCTTTTTA
Found at i:26201 original size:6 final size:6
Alignment explanation
Indices: 26190--26219 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
26180 TCTTTTTCAC
26190 AACCCA AACCCA AACCCA AACCCA AACCCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA
26220 GATCTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCCA
Found at i:33131 original size:22 final size:22
Alignment explanation
Indices: 33080--33133 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
33070 AAAAAATTTT
*
33080 ATATT-AATAAATTTAACATTAA
1 ATATTAAAT-AATTTAACAATAA
*
33102 A-ATAAAATAATTTAACAATAA
1 ATATTAAATAATTTAACAATAA
33123 ATATTAAATAA
1 ATATTAAATAA
33134 ATAATCTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATTAAATAATTTAACAATAA
Done.