Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004327.1 Kokia drynarioides strain JFW-HI SEQ_117651, 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: 15554
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2370 original size:10 final size:10
Alignment explanation
Indices: 2355--2388 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2345 AATTTGAATT
2355 TTATATTTTA
1 TTATATTTTA
2365 TTATATTTTA
1 TTATATTTTA
2375 -TATATTATTA
1 TTATATT-TTA
2385 TTAT
1 TTAT
2389 TTATAATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 13 0.59
11 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATATTTTA
Found at i:2372 original size:17 final size:18
Alignment explanation
Indices: 2352--2390 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2342 TCGAATTTGA
*
2352 ATTTTATATTTTATTA-T
1 ATTTTATATATTATTATT
2369 ATTTTATATATTATTATT
1 ATTTTATATATTATTATT
2387 ATTT
1 ATTT
2391 ATAATAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTATATATTATTATT
Found at i:2691 original size:45 final size:46
Alignment explanation
Indices: 2627--2717 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 46
2617 GGTTTTTGCG
*
2627 TGTGGTCTTTATTATTACGTTATCATA-TTT-GATCATTTCATTGTC
1 TGTGGTCTTTATTATTACGTTAACATATTTTCG-TCATTTCATTGTC
2672 TGTGGTCTTTATTATTACGTTAACATATTTTCGTCATTTCATTGTC
1 TGTGGTCTTTATTATTACGTTAACATATTTTCGTCATTTCATTGTC
2718 GATCTATTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
45 26 0.60
46 16 0.37
47 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.13, T:0.53
Consensus pattern (46 bp):
TGTGGTCTTTATTATTACGTTAACATATTTTCGTCATTTCATTGTC
Found at i:8558 original size:29 final size:30
Alignment explanation
Indices: 8536--8736 Score: 171
Period size: 29 Copynumber: 6.8 Consensus size: 30
8526 TTTAGGCGAA
8536 TTCGAGGTTAAAATGTAATTTTA-GAAAAG
1 TTCGAGGTTAAAATGTAATTTTAGGAAAAG
* * *
8565 TTTGAGGTCAAAATGTGATTTTAGG-AAAG
1 TTCGAGGTTAAAATGTAATTTTAGGAAAAG
** * *
8594 TTTAAAGGTTAAAATGTGATTTT-GGGAAAG
1 -TTCGAGGTTAAAATGTAATTTTAGGAAAAG
* * *
8624 TTTGGGGGTTAAAATGTAATTTT-GGAGAAG
1 -TTCGAGGTTAAAATGTAATTTTAGGAAAAG
* * *
8654 TTTGGGGTTAAAATGTGATTTT-GGAAAAG
1 TTCGAGGTTAAAATGTAATTTTAGGAAAAG
* *
8683 TTCAAGGTTAAAATATAATTTTAGG-AAAG
1 TTCGAGGTTAAAATGTAATTTTAGGAAAAG
* * *
8712 TTTAGGGGTCAAAATGTAATTTTAG
1 -TTCGAGGTTAAAATGTAATTTTAG
8737 AGTAGGTTAG
Statistics
Matches: 142, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
29 73 0.51
30 69 0.49
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (30 bp):
TTCGAGGTTAAAATGTAATTTTAGGAAAAG
Found at i:8610 original size:30 final size:29
Alignment explanation
Indices: 8541--8891 Score: 280
Period size: 30 Copynumber: 11.9 Consensus size: 29
8531 GCGAATTCGA
* * *
8541 GGTTAAAATGTAATTTTAGAAAAGTTT-GA
1 GGTTAAAATGTGATTTT-GGAAAGTTTAGG
* **
8570 GGTCAAAATGTGATTTTAGGAAAGTTTAAA
1 GGTTAAAATGTGATTTT-GGAAAGTTTAGG
*
8600 GGTTAAAATGTGATTTTGGGAAAGTTTGGG
1 GGTTAAAATGTGATTTT-GGAAAGTTTAGG
*
8630 GGTTAAAATGTAATTTTGGAGAAGTTT-GG
1 GGTTAAAATGTGATTTTGGA-AAGTTTAGG
* *
8659 GGTTAAAATGTGATTTTGGAAAAGTTCA-A
1 GGTTAAAATGTGATTTTGG-AAAGTTTAGG
* *
8688 GGTTAAAATATAATTTTAGGAAAGTTTAGG
1 GGTTAAAATGTGATTTT-GGAAAGTTTAGG
* * * * *
8718 GGTCAAAATGTAATTTTAGAGTAGGTTAGG
1 GGTTAAAATGTGATTTTGGA-AAGTTTAGG
* * * *
8748 GGTCAAAATGTAATTTTGGGAAGTTTATG
1 GGTTAAAATGTGATTTTGGAAAGTTTAGG
* **
8777 GG-TCAAATGTGATTTTGGGAAAGTTTAAA
1 GGTTAAAATGTGATTTT-GGAAAGTTTAGG
* * **
8806 GGTCAAAATGAGATTTTCTAAAAGTTTAGG
1 GGTTAAAATGTGATTTT-GGAAAGTTTAGG
*
8836 GGTTAAAATGTTATTTTGGAGAAGTTT-GAG
1 GGTTAAAATGTGATTTTGGA-AAGTTTAG-G
* *
8866 GGTCAAAATGTGATTTCTTGAAAGTT
1 GGTTAAAATGTGATTT-TGGAAAGTT
8892 CAAGGACCTA
Statistics
Matches: 261, Mismatches: 49, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
28 11 0.04
29 97 0.37
30 150 0.57
31 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
GGTTAAAATGTGATTTTGGAAAGTTTAGG
Found at i:8726 original size:118 final size:118
Alignment explanation
Indices: 8541--8881 Score: 377
Period size: 118 Copynumber: 2.9 Consensus size: 118
8531 GCGAATTCGA
* * ** * * **
8541 GGTTAAAATGTAATTTTAGAAAAGTTTGAGGTCAAAATGTGATTTTAGGAAAGTTTAAAGGTTAA
1 GGTTAAAATGTGATTTTGGAAAAGTTAAAGGTCAAAATATAATTTTAGGAAAGTTTAGGGGTTAA
* *
8606 AATGTGATTTTGG-GAAAGTTTGGGGGTTAAAATGTAATTTTGGAGAAGTTT-GG
66 AATGTAATTTTGGAG-AAGTTTGGGGGTCAAAATGTAATTTTGG-GAAGTTTAGG
* * *
8659 GGTTAAAATGTGATTTTGGAAAAGTTCAAGGTTAAAATATAATTTTAGGAAAGTTTAGGGGTCAA
1 GGTTAAAATGTGATTTTGGAAAAGTTAAAGGTCAAAATATAATTTTAGGAAAGTTTAGGGGTTAA
* * * * *
8724 AATGTAATTTTAGAGTAGGTTAGGGGTCAAAATGTAATTTTGGGAAGTTTATG
66 AATGTAATTTTGGAGAAGTTTGGGGGTCAAAATGTAATTTTGGGAAGTTTAGG
* * * *
8777 GG-TCAAATGTGATTTTGGGAAAGTTTAAAGGTCAAAATGAGATTTTCTA--AAAGTTTAGGGGT
1 GGTTAAAATGTGATTTTGGAAAAG-TTAAAGGTCAAAAT-ATAATTT-TAGGAAAGTTTAGGGGT
* * *
8839 TAAAATGTTATTTTGGAGAAGTTTGAGGGTCAAAATGTGATTT
63 TAAAATGTAATTTTGGAGAAGTTTGGGGGTCAAAATGTAATTT
8882 CTTGAAAGTT
Statistics
Matches: 187, Mismatches: 31, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
117 26 0.14
118 153 0.82
119 6 0.03
120 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (118 bp):
GGTTAAAATGTGATTTTGGAAAAGTTAAAGGTCAAAATATAATTTTAGGAAAGTTTAGGGGTTAA
AATGTAATTTTGGAGAAGTTTGGGGGTCAAAATGTAATTTTGGGAAGTTTAGG
Found at i:8729 original size:88 final size:87
Alignment explanation
Indices: 8545--8881 Score: 343
Period size: 88 Copynumber: 3.8 Consensus size: 87
8535 ATTCGAGGTT
*
8545 AAAATGTAATTTTAGAAAAGTTTGAGGTCAAAATGTGATTTTAGGAAAGTTTAAAGGTTAAAATG
1 AAAATGTAATTTTAGAAAAGTTTGGGGTCAAAATGTGATTTT-GGAAAG-TTAAAGGTTAAAATG
* *
8610 TGATTTTGGGAAAGTTTGGGGGTT
64 TGATTTTGGGAAAGTTTAGGGGTC
* * * * *
8634 AAAATGTAATTTTGGAGAAGTTTGGGGTTAAAATGTGATTTTGGAAAAGTTCAAGGTTAAAATAT
1 AAAATGTAATTTTAGAAAAGTTTGGGGTCAAAATGTGATTTTGG-AAAGTTAAAGGTTAAAATGT
* *
8699 AATTTTAGGAAAGTTTAGGGGTC
65 GATTTTGGGAAAGTTTAGGGGTC
* * * * * * * * *
8722 AAAATGTAATTTTAGAGTAGGTTAGGGGTCAAAATGTAATTTTGGGAAGTTTATGGGTCAAATGT
1 AAAATGTAATTTTAGA-AAAGTTTGGGGTCAAAATGTGATTTTGGAAAGTTAAAGGTTAAAATGT
**
8787 GATTTTGGGAAAGTTTAAAGGTC
65 GATTTTGGGAAAGTTTAGGGGTC
** * * * * *
8810 AAAATG-AGATTTTCTAAAAGTTTAGGGGTTAAAATGTTATTTTGGAGAAGTTTGAGGGTCAAAA
1 AAAATGTA-ATTTTAGAAAAGTTT-GGGGTCAAAATGTGATTTTGGA-AAG-TTAAAGGTTAAAA
8874 TGTGATTT
62 TGTGATTT
8882 CTTGAAAGTT
Statistics
Matches: 203, Mismatches: 39, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
87 5 0.02
88 114 0.56
89 68 0.33
90 16 0.08
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (87 bp):
AAAATGTAATTTTAGAAAAGTTTGGGGTCAAAATGTGATTTTGGAAAGTTAAAGGTTAAAATGTG
ATTTTGGGAAAGTTTAGGGGTC
Found at i:10697 original size:50 final size:49
Alignment explanation
Indices: 10633--11152 Score: 399
Period size: 50 Copynumber: 10.5 Consensus size: 49
10623 TATTGGATTT
*
10633 ACCGTTGCGACCTCAATCCTTT-CTATCGCATCTT-TTAAGGTACCGGGTTC
1 ACCGTTGCGGCCTCAA-CCTTTCCT-TCGCATCTTCTT-AGGTACCGGGTTC
* * * *
10683 ATCGTTACGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTATCGGGTTC
1 ACCGTTGCGGCCTCAACCTTT-CCTTCGCATCTTCTTAGGTACCGGGTTC
* * * ** * *
10733 GCCGTTGCAGCCTCAACTTTTCCCTTCTTATCTTCAT-GGTACCAGGTT-
1 ACCGTTGCGGCCTCAACCTTT-CCTTCGCATCTTCTTAGGTACCGGGTTC
* * * *
10781 AGCCGTTGTGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTATCGGGTTT
1 A-CCGTTGCGGCCTCAACCTTT-CCTTCGCATCTTCTTAGGTACCGGGTTC
* * *
10832 GCCGTTGCAGCCTCAACCTTTCCCTTCGTATCTTCTTAGGTACCGGGTTC
1 ACCGTTGCGGCCTCAACCTTT-CCTTCGCATCTTCTTAGGTACCGGGTTC
* * * *
10882 ACCGTTTCGGTCTCAACCTTTCCCTTCGCATCTTCTTAGGTACCGGCTTT
1 ACCGTTGCGGCCTCAACCTTT-CCTTCGCATCTTCTTAGGTACCGGGTTC
** ** *
10932 ACCGTTGCAACCTCAATCCTTTCCTTCAAATCTTCAT-GGTACCGGGTTC
1 ACCGTTGCGGCCTCAA-CCTTTCCTTCGCATCTTCTTAGGTACCGGGTTC
** * * * *
10981 GTCGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTAGGTACTGGGTTT
1 ACCGTTGCGGCCTCAACCTTT-CCTTCGCATCTTCTTAGGTACCGGGTTC
* * * * * * *
11030 ATCGTTGCGACCTCAACCTTTCTCTTTGTATATTCAT-GGTACCGAGTTC
1 ACCGTTGCGGCCTCAACCTTTC-CTTCGCATCTTCTTAGGTACCGGGTTC
* * * * * *
11079 GCCGTTGTAGTCCTCAACCTTTCCCATT-ACATCTTCTAAGGTACTGGGTTC
1 ACCGTTG-CGGCCTCAACCTTT-CC-TTCGCATCTTCTTAGGTACCGGGTTC
* * *
11130 GCCATTGTGGCCTCAACCTTTCC
1 ACCGTTGCGGCCTCAACCTTTCC
11153 CTTCATATCT
Statistics
Matches: 372, Mismatches: 83, Indels: 31
0.77 0.17 0.06
Matches are distributed among these distances:
48 7 0.02
49 126 0.34
50 212 0.57
51 27 0.07
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (49 bp):
ACCGTTGCGGCCTCAACCTTTCCTTCGCATCTTCTTAGGTACCGGGTTC
Found at i:10774 original size:99 final size:98
Alignment explanation
Indices: 10671--11162 Score: 526
Period size: 99 Copynumber: 5.0 Consensus size: 98
10661 CATCTTTTAA
* *
10671 GGTACCGGGTTCATCGTTACGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTATCGGGTTCGCC
1 GGTACCGGGTTCACCGTTACGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTA-CGGGTTTGCC
* *
10736 GTTGCAGCCTCAACTTTTCCCTTCTTATCTTCAT
65 GTTGCAGCCTCAACCTTTCCCTTCATATCTTCAT
* **
10770 GGTACCAGGTT-AGCCGTTGTGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTATCGGGTTTGC
1 GGTACCGGGTTCA-CCGTTACGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTA-CGGGTTTGC
* *
10834 CGTTGCAGCCTCAACCTTTCCCTTCGTATCTTCTT
64 CGTTGCAGCCTCAACCTTTCCCTTCATATCTTCAT
* * * * *
10869 AGGTACCGGGTTCACCGTTTCGGTCTCAACCTTTCCCTTCGCATCTTCTTAGGTACCGGCTTTAC
1 -GGTACCGGGTTCACCGTTACGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTA-CGGGTTTGC
* *
10934 CGTTGCAACCTCAATCCTTT-CCTTCAAATCTTCAT
64 CGTTGCAGCCTCAA-CCTTTCCCTTCATATCTTCAT
** * * **
10969 GGTACCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTAGGTACTGGGTTTATC
1 GGTACCGGGTTCACCGTTACGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTAC-GGGTTTGCC
* ** *
11033 GTTGC-GACCTCAACCTTTCTCTTTGTATATTCAT
65 GTTGCAG-CCTCAACCTTTCCCTTCATATCTTCAT
* * * ** * *
11067 GGTACCGAGTTCGCCGTTGTA-GTCCTCAACCTTTCCCATTACATCTTCTAAGGTACTGGGTTCG
1 GGTACCGGGTTCACCG-T-TACGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTAC-GGGTTTG
* **
11131 CCATTGTGGCCTCAACCTTTCCCTTCATATCT
63 CCGTTGCAGCCTCAACCTTTCCCTTCATATCT
11163 CCAGGGTATT
Statistics
Matches: 333, Mismatches: 49, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
97 6 0.02
98 50 0.15
99 154 0.46
100 116 0.35
101 7 0.02
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (98 bp):
GGTACCGGGTTCACCGTTACGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTACGGGTTTGCCG
TTGCAGCCTCAACCTTTCCCTTCATATCTTCAT
Found at i:10849 original size:149 final size:146
Alignment explanation
Indices: 10593--11153 Score: 533
Period size: 149 Copynumber: 3.8 Consensus size: 146
10583 CGCCATTATG
** *
10593 GCCTCAACCTTTCCCTTTATATCTTCATGGTATTGGATTTACCGTTGCGACCTCAATCCTTTCTA
1 GCCTCAACCTTTCCCTTTATATCTTCATGGTACCGG-TTTACCGTTGCGACCTCAATCCTTTCCA
* ** *
10658 TCGCATCTT-TTAAGGTACCGGGTTCATCGTTACGGCCTCAACCTTTCCCATCGCATCTTCTTAG
65 TCACATCTTCTT-AGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCGCATCTTCTTAG
*
10722 GTATCGGGTTCGCCGTTGC
129 GTA-CGGGTTCACCGTTGC
* * *
10741 AGCCTCAACTTTTCCCTTCT-TATCTTCATGGTACCAGG-TTAGCCGTTGTGGCCTCAA-CCTTT
1 -GCCTCAACCTTTCCCTT-TATATCTTCATGGTACC-GGTTTA-CCGTTGCGACCTCAATCCTTT
* * * * * *
10803 CCCATCGCATCTTCTTAGGTATCGGGTTTGCCGTTGCAGCCTCAACCTTTCCCTTCGTATCTTCT
62 -CCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCGCATCTTCT
*
10868 TAGGTACCGGGTTCACCGTTTC
126 TAGGTA-CGGGTTCACCGTTGC
* *** * *
10890 GGTCTCAACCTTTCCCTTCGCATCTTCTTAGGTACCGGCTTTACCGTTGCAACCTCAATCCTTTC
1 -GCCTCAACCTTTCCCTTTATATCTTCAT-GGTACCGG-TTTACCGTTGCGACCTCAATCCTTTC
* * * * *
10955 CTTCAAATCTTCAT-GGTACCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTA
63 CATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCGCATCTTCTTA
* *
11018 GGTACTGGGTTTATCGTTGC
128 GGTAC-GGGTTCACCGTTGC
* * * ** * *
11038 GACCTCAACCTTTCTCTTTGTATATTCATGGTACCGAGTTCGCCGTTGTAGTCCTCAA-CCTTTC
1 G-CCTCAACCTTTCCCTTTATATCTTCATGGTACCG-GTTTACCGTTG-CGACCTCAATCCTTT-
* * * * *
11102 CCATTACATCTTCTAAGGTACTGGGTTCGCCATTGTGGCCTCAACCTTTCCC
62 CCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
11154 TTCATATCTC
Statistics
Matches: 336, Mismatches: 60, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
147 22 0.07
148 64 0.19
149 208 0.62
150 34 0.10
151 8 0.02
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.36
Consensus pattern (146 bp):
GCCTCAACCTTTCCCTTTATATCTTCATGGTACCGGTTTACCGTTGCGACCTCAATCCTTTCCAT
CACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCGCATCTTCTTAGGT
ACGGGTTCACCGTTGC
Done.