Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003054.1 Kokia drynarioides strain JFW-HI SEQ_115582, 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: 6283
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:135 original size:78 final size:77
Alignment explanation
Indices: 45--326 Score: 244
Period size: 78 Copynumber: 3.6 Consensus size: 77
35 AAAATCACCG
* * *
45 TCAGCCAATCTCTTACTCCGAGCTTCGGGTAGATTGCAGCCATTCAATCTCTTACCCCGAGTTTG
1 TCAGCCAATCTCTTAC-CCGAGCTTCGGGTAGATTGCAGCCATTCGATCTATTACCCCGAGCTTG
110 GGGTCGATCTCCA
65 GGGTCGATCTCCA
* * * * * * * ** * *
123 TCAGCTAATCTCTTACCCCAAGCCTCGAGTAGATTACAGCCTTTCGATCTTTTACCCTTACCCT-
1 TCAGCCAATCTCTTA-CCCGAGCTTCGGGTAGATTGCAGCCATTCGATCTATTACCCCGAGCTTG
*
187 GGGACAGATCAT-CA
65 GGGTC-GATC-TCCA
* * * * *
201 TCAGCCAATCTCTTACCTCGATCTTAGGGCAAATTGCAGCCATTCGATCTATTACCCCGAGCCTG
1 TCAGCCAATCTCTTACC-CGAGCTTCGGGTAGATTGCAGCCATTCGATCTATTACCCCGAG-CTT
* *
266 GGGGTAGATCACCA
64 GGGGTCGATCTCCA
* * * * *
280 TCAGCCAATCTCTTACCTCGATCATGGGGCAGATTGCAGGCATTCGA
1 TCAGCCAATCTCTTACC-CGAGCTTCGGGTAGATTGCAGCCATTCGA
327 AGCAATAAAG
Statistics
Matches: 160, Mismatches: 37, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
77 6 0.04
78 99 0.62
79 52 0.32
80 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (77 bp):
TCAGCCAATCTCTTACCCGAGCTTCGGGTAGATTGCAGCCATTCGATCTATTACCCCGAGCTTGG
GGTCGATCTCCA
Found at i:751 original size:6 final size:6
Alignment explanation
Indices: 740--823 Score: 70
Period size: 6 Copynumber: 14.7 Consensus size: 6
730 GACCCATTTG
* * *
740 TTAAAT TTAAAT TT-AAT TTAAGT TTAAAT TT-AGT TTAAAT ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
786 TT-ATT TTGAAT TTAAA- TT-CAT TATAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTAA
824 TTAAAAATTA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
4 1 0.02
5 16 0.26
6 41 0.67
7 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:765 original size:17 final size:17
Alignment explanation
Indices: 740--825 Score: 102
Period size: 17 Copynumber: 5.1 Consensus size: 17
730 GACCCATTTG
740 TTAAATTTAAATTTAAT
1 TTAAATTTAAATTTAAT
* *
757 TTAAGTTTAAATTTAGT
1 TTAAATTTAAATTTAAT
* *
774 TTAAATATAAATTTATT
1 TTAAATTTAAATTTAAT
* *
791 TTGAATTTAAA-TTCAT
1 TTAAATTTAAATTTAAT
807 TATAAATTTAAATTTAAT
1 T-TAAATTTAAATTTAAT
825 T
1 T
826 AAAAATTATA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
16 4 0.07
17 47 0.84
18 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAAATTTAAATTTAAT
Found at i:2258 original size:36 final size:36
Alignment explanation
Indices: 2201--2303 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
2191 GGTATTTATA
* * * *
2201 GGGCATCAAAACGACGTCGTTTTGGCCTTGGTGCCT
1 GGGCCTCAAAACGACGCCGTTTTGGCCTTAGTGCCC
2237 GGGCCTCAAAACGACGCCGTTTTGGCCTTAGTGCCC
1 GGGCCTCAAAACGACGCCGTTTTGGCCTTAGTGCCC
* * *
2273 AGGCCTAAAAATGACGCCGTTTTGAGCCTTA
1 GGGCCTCAAAACGACGCCGTTTTG-GCCTTA
2304 CCCATTTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 53 0.90
37 6 0.10
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (36 bp):
GGGCCTCAAAACGACGCCGTTTTGGCCTTAGTGCCC
Found at i:2827 original size:29 final size:29
Alignment explanation
Indices: 2701--2886 Score: 164
Period size: 30 Copynumber: 6.3 Consensus size: 29
2691 TAAAAGGTCC
* *
2701 CTAAACTTTCCAAAAATCACATTTTAGCCC-
1 CTAAACTTTTC-AAAATTACATTTT-GCCCT
* ** *
2731 CTAAACTTTTCCAAAATTGCATTTTAACCA
1 CTAAACTTTT-CAAAATTACATTTTGCCCT
* *
2761 CTAAACTTTTCCAAAATTTCATTTTCCCCT
1 CTAAACTTTT-CAAAATTACATTTTGCCCT
2791 -TAAACTTTTCAAAATTACATTTTGCCCT
1 CTAAACTTTTCAAAATTACATTTTGCCCT
* *
2819 CTAATCTTTTCAAAAATTACATTTTTACCC-
1 CTAAACTTTTC-AAAATTACA-TTTTGCCCT
* *
2849 CCAAACTTCTTTAAAATTACATTTTTGCCCT
1 CTAAACTT-TTCAAAATTACA-TTTTGCCCT
2880 C-AAACTT
1 CTAAACTT
2887 CAAAAAATTA
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
28 17 0.13
29 20 0.15
30 84 0.64
31 11 0.08
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (29 bp):
CTAAACTTTTCAAAATTACATTTTGCCCT
Found at i:2828 original size:58 final size:59
Alignment explanation
Indices: 2701--2907 Score: 210
Period size: 58 Copynumber: 3.5 Consensus size: 59
2691 TAAAAGGTCC
* * * ** *
2701 CTAAACTTTCCAAAAATCACA-TTTTAGCCCCTAAACTTTTCCAAAATTGCATTTTAACCA
1 CTAAACTTTTCAAAAATTACATTTTTA-CCCCTAAACTTTT-CAAAATTACATTTTGCCCT
* *
2761 CTAAACTTTTCCAAAATTTCA-TTTT-CCCCTTAAACTTTTCAAAATTACATTTTGCCCT
1 CTAAACTTTTCAAAAATTACATTTTTACCCC-TAAACTTTTCAAAATTACATTTTGCCCT
* * *
2819 CTAATCTTTTCAAAAATTACATTTTTACCCCCAAACTTCTTTAAAATTACATTTTTGCCCT
1 CTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTT-TTCAAAATTACA-TTTTGCCCT
*
2880 C-AAAC--TTCAAAAAATTAAATTTTTACCC
1 CTAAACTTTTC-AAAAATTACATTTTTACCC
2908 TCGAACTTCT
Statistics
Matches: 126, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
58 40 0.32
59 37 0.29
60 39 0.31
61 10 0.08
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (59 bp):
CTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTTTCAAAATTACATTTTGCCCT
Found at i:2855 original size:88 final size:89
Alignment explanation
Indices: 2702--2873 Score: 215
Period size: 88 Copynumber: 1.9 Consensus size: 89
2692 AAAAGGTCCC
* * *
2702 TAAACTTTCCAAAAATCACATTTTAGCCCCTAAACTTTTCCAAAATTGCATTTTAACCACTAAAC
1 TAAACTTTCCAAAAATCACATTTTAGCCCCTAAACTTTTCAAAAATTACATTTTAACCACCAAAC
*
2767 TT-TTCCAAAATTTCATTTTCCCCT
66 TTCTT-CAAAATTACATTTTCCCCT
* * * * *
2791 TAAACTTTTC-AAAATTACATTTT-GCCCTCTAATCTTTTCAAAAATTACATTTTTACCCCCAAA
1 TAAACTTTCCAAAAATCACATTTTAGCCC-CTAAACTTTTCAAAAATTACATTTTAACCACCAAA
*
2854 CTTCTTTAAAATTACATTTT
65 CTTCTTCAAAATTACATTTT
2874 TGCCCTCAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
87 4 0.06
88 56 0.79
89 11 0.15
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (89 bp):
TAAACTTTCCAAAAATCACATTTTAGCCCCTAAACTTTTCAAAAATTACATTTTAACCACCAAAC
TTCTTCAAAATTACATTTTCCCCT
Found at i:2894 original size:29 final size:29
Alignment explanation
Indices: 2699--3169 Score: 178
Period size: 29 Copynumber: 16.3 Consensus size: 29
2689 CTTAAAAGGT
*
2699 CCCT-AAACTTTCCAAAAATCACA-TTTTA
1 CCCTCAAAC-TTCCAAAAATTACATTTTTA
* *
2727 GCCC-CTAAACTTTTCC-AAAATTGCATTTTAA
1 -CCCTC-AAAC--TTCCAAAAATTACATTTTTA
* *
2758 CCACT-AAACTTTTCC-AAAATTTCA-TTTTC
1 CC-CTCAAAC--TTCCAAAAATTACATTTTTA
* * *
2787 CCCTTAAACTTTTC-AAAATTACA-TTTTG
1 CCCTCAAAC-TTCCAAAAATTACATTTTTA
* *
2815 CCCTCTAATCTTTTCAAAAATTACATTTTTA
1 CCCTC-AAAC-TTCCAAAAATTACATTTTTA
* ** *
2846 CCCCCAAACTTCTTTAAAATTACATTTTTG
1 CCCTCAAACTTC-CAAAAATTACATTTTTA
* *
2876 CCCTCAAACTTCAAAAAATTAAATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* * *
2905 CCCTCGAACTTCTAAAAATCACATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* * * * *
2934 GACC-CGAACATCCAAAAATCATATTTTTA
1 -CCCTCAAACTTCCAAAAATTACATTTTTA
*
2963 CCCTCAAACATCCAAAAATTAC-TATTTTA
1 CCCTCAAACTTCCAAAAATTACAT-TTTTA
* * *
2992 TCC-CAAA-TATCTAAAAAGATTATCATTTTGA
1 CCCTCAAACT-TC-CAAAA-ATTA-CATTTTTA
* * *
3023 CTC-CAAACTTTTCTAAAATTACCA-TTTTA
1 CCCTCAAAC-TTCCAAAAATTA-CATTTTTA
* * * *
3052 CCCACGAACGTCCAAAAATTGCATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* *
3081 ---T---ACATCCAAAAATTACCA-TTTTG
1 CCCTCAAACTTCCAAAAATTA-CATTTTTA
* * **
3104 CCCTCGAACATCCAAATTTTACCATTTTT-
1 CCCTCAAACTTCCAAAAATTA-CATTTTTA
* * *
3133 CCCTCAAATTTCCAAAAATCACATTTTCA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
*
3162 ACCTCAAA
1 CCCTCAAA
3170 TTTTAAGAAA
Statistics
Matches: 344, Mismatches: 66, Indels: 64
0.73 0.14 0.14
Matches are distributed among these distances:
23 16 0.05
24 2 0.01
26 1 0.00
28 39 0.11
29 164 0.48
30 88 0.26
31 31 0.09
32 2 0.01
33 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTTA
Found at i:2896 original size:59 final size:60
Alignment explanation
Indices: 2792--2932 Score: 166
Period size: 59 Copynumber: 2.4 Consensus size: 60
2782 TTTTCCCCTT
* * *
2792 AAACTT-TTCAAAATTACA-TTTTGCCCTCTAATCTTTTCAAAAATTACATTTTTACCCCC
1 AAACTTCTTAAAAATTACATTTTTGCCCTCTAAAC-TTTCAAAAATTAAATTTTTACCCCC
* *
2851 AAACTTCTTTAAAATTACATTTTTGCCCTC-AAAC-TTCAAAAAATTAAATTTTTACCCTC
1 AAACTTCTTAAAAATTACATTTTTGCCCTCTAAACTTTC-AAAAATTAAATTTTTACCCCC
* *
2910 GAACTTC-TAAAAATCACATTTTT
1 AAACTTCTTAAAAATTACATTTTT
2933 AGACCCGAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
58 17 0.24
59 31 0.43
60 14 0.19
61 10 0.14
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (60 bp):
AAACTTCTTAAAAATTACATTTTTGCCCTCTAAACTTTCAAAAATTAAATTTTTACCCCC
Found at i:3217 original size:29 final size:30
Alignment explanation
Indices: 3134--3218 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
3124 ACCATTTTTC
3134 CCTCAAA-TTTCCAAAAA-TCACATTTTCAA
1 CCTCAAATTTTCCAAAAATTCA-ATTTTCAA
*
3163 CCTCAAATTTT--AAGAAAGTTCGATTTT-AA
1 CCTCAAATTTTCCAA-AAA-TTCAATTTTCAA
*
3192 TCTCAAATTTTCCAAAAATTCAATTTT
1 CCTCAAATTTTCCAAAAATTCAATTTT
3219 GTTCCCCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
28 2 0.04
29 30 0.64
30 11 0.23
31 4 0.09
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (30 bp):
CCTCAAATTTTCCAAAAATTCAATTTTCAA
Done.