Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014257.1 Kokia drynarioides strain JFW-HI SEQ_129290, 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: 9750
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Found at i:538 original size:16 final size:16
Alignment explanation
Indices: 478--530 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
468 AACAGTTTTT
*
478 ATAATAATTATTAATA
1 ATAATAATAATTAATA
* **
494 ATAAATATTTTCTTAATA
1 AT-AATA-ATAATTAATA
512 ATAATAATAATTAATA
1 ATAATAATAATTAATA
528 ATA
1 ATA
531 TGATTAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 12 0.40
17 8 0.27
18 10 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATAATAATTAATA
Found at i:754 original size:117 final size:116
Alignment explanation
Indices: 607--903 Score: 540
Period size: 117 Copynumber: 2.6 Consensus size: 116
597 AGGGTGAGGC
607 GACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACT
1 GACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACT
* *
672 TACCAGGATTCCCTTAGTAACGGTGAGCGAACCGGGAAAAGCCCAGCTTGGT
66 TACCAGGATTCCCTTAGTAACGGCGAGCGAACCGGGAAAAG-CCAGCATGGT
*
724 GTCCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACT
1 GACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACT
*
789 TACCAGGATTCCCTTAGTAACGGCGAGTGAACCGGGAAAAGCCAGCATGGT
66 TACCAGGATTCCCTTAGTAACGGCGAGCGAACCGGGAAAAGCCAGCATGGT
*
840 GACCCCAGGTCAGGCGGGATTACCCGCTGAGCTTAAGCATATCAATAAGCGGAGGAAAAGAAAC
1 GACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAAC
904 CCTTACCTGA
Statistics
Matches: 174, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
116 71 0.41
117 103 0.59
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (116 bp):
GACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACT
TACCAGGATTCCCTTAGTAACGGCGAGCGAACCGGGAAAAGCCAGCATGGT
Found at i:1676 original size:29 final size:29
Alignment explanation
Indices: 1643--2011 Score: 248
Period size: 29 Copynumber: 12.6 Consensus size: 29
1633 CCCTAAGCTG
*
1643 TCCAAAAATTCTATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACT
*
1672 TCC-AAAATTCCATTTTTAGCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACT
1700 TCCAAAAA-TCCTATTTTTTACCC-CGAAACT
1 TCCAAAAATTCC-A-TTTTTACCCTCG-AACT
*
1730 TCCCAAAATTCCATTTTTAGCCCT-GAACT
1 TCCAAAAATTCCATTTTTA-CCCTCGAACT
*
1759 TCCAAAAATTCCATTTTTAGCCC-CAAACT
1 TCCAAAAATTCCATTTTTA-CCCTCGAACT
* ** *
1788 TCCAAAAA-TCTCATTTTTAACCTTAAAATT
1 TCCAAAAATTC-CATTTTT-ACCCTCGAACT
1818 TCTC-AAAATTCCATTTTTAGCCC-CGAACT
1 TC-CAAAAATTCCATTTTTA-CCCTCGAACT
1847 TCCAAAAA-TCTCATTTTTGA-CCTCGAAACT
1 TCCAAAAATTC-CATTTTT-ACCCTCG-AACT
* * *
1877 TCCTAAAATTACCA-TTTTACCCCCGGA-T
1 TCCAAAAATT-CCATTTTTACCCTCGAACT
* * *
1905 GTCTAAAAACTCCATTTTTTA-CTTCGAAACT
1 -TCCAAAAATTCCA-TTTTTACCCTCG-AACT
* * * *
1936 TCCTAAAATTACC-CTTTTACCC-CTAAAT
1 TCCAAAAATT-CCATTTTTACCCTCGAACT
* *
1964 GTCTAAAAATTCCATTTTTAACCCT-GAATTT
1 -TCCAAAAATTCCATTTTT-ACCCTCGAA-CT
*
1995 TCCCAAAATTACCATTT
1 TCCAAAAATT-CCATTT
2012 CACCCCCGAG
Statistics
Matches: 269, Mismatches: 36, Indels: 68
0.72 0.10 0.18
Matches are distributed among these distances:
28 45 0.17
29 112 0.42
30 92 0.34
31 19 0.07
32 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.36
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCTCGAACT
Found at i:1793 original size:88 final size:88
Alignment explanation
Indices: 1647--1864 Score: 291
Period size: 88 Copynumber: 2.5 Consensus size: 88
1637 AAGCTGTCCA
* * *
1647 AAAATTCTATTTTTA-CCCTCGAACTTCC-AAAATTCCATTTTTAGCCTCGAACTTCCAAAAATC
1 AAAATTCCATTTTTAGCCCT-GAACTTCCAAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATC
* *
1710 -CTATTTTTTACCCCGAAACTTCCC
65 TC-ATTTTTAACCCCAAAACTTCCC
1734 AAAATTCCATTTTTAGCCCTGAACTTCCAAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATCT
1 AAAATTCCATTTTTAGCCCTGAACTTCCAAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATCT
** * *
1799 CATTTTTAACCTTAAAATTTCTC
66 CATTTTTAACCCCAAAACTTCCC
*
1822 AAAATTCCATTTTTAGCCCCGAACTTCCAAAAA-TCTCATTTTT
1 AAAATTCCATTTTTAGCCCTGAACTTCCAAAAATTC-CATTTTT
1865 GACCTCGAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
87 24 0.21
88 92 0.79
89 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (88 bp):
AAAATTCCATTTTTAGCCCTGAACTTCCAAAAATTCCATTTTTAGCCCCAAACTTCCAAAAATCT
CATTTTTAACCCCAAAACTTCCC
Found at i:1895 original size:59 final size:59
Alignment explanation
Indices: 1647--1986 Score: 287
Period size: 59 Copynumber: 5.8 Consensus size: 59
1637 AAGCTGTCCA
* *
1647 AAAATTCTATTTTTACCCTCGAACTTCC-AAAAT-TCCATTTTTAGCCTCG-AACTTCC-
1 AAAATTCCATTTTTACCC-CGAACTTCCAAAAATCTCCATTTTTAACCTCGAAACTTCCT
* * * *
1703 AAAAATCCTATTTTTTACCCCGAAACTTCCCAAAAT-TCCATTTTTAGCC-CTG-AACTTCCA
1 AAAATTCC-A-TTTTTACCCCG-AACTTCCAAAAATCTCCATTTTTAACCTC-GAAACTTCCT
* * * *
1763 AAAATTCCATTTTTAGCCCCAAACTTCCAAAAATCT-CATTTTTAACCT-TAAAATTTCT
1 AAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCTCCATTTTTAACCTCGAAACTTCCT
*
1821 CAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATCT-CATTTTTGACCTCGAAACTTCCT
1 -AAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCTCCATTTTTAACCTCGAAACTTCCT
* * * *
1881 AAAATTACCA-TTTTACCCCCGGA-TGTCTAAAAA-CTCCATTTTTTACTTCGAAACTTCCT
1 AAAATT-CCATTTTTA-CCCCGAACT-TCCAAAAATCTCCATTTTTAACCTCGAAACTTCCT
* * * *
1940 AAAATTACC-CTTTTACCCCTAAATGTCTAAAAAT-TCCATTTTTAACC
1 AAAATT-CCATTTTTACCCCGAACT-TCCAAAAATCTCCATTTTTAACC
1987 CTGAATTTTC
Statistics
Matches: 242, Mismatches: 24, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
56 6 0.02
57 3 0.01
58 58 0.24
59 158 0.65
60 17 0.07
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAATTCCATTTTTACCCCGAACTTCCAAAAATCTCCATTTTTAACCTCGAAACTTCCT
Found at i:2003 original size:59 final size:56
Alignment explanation
Indices: 1715--2017 Score: 211
Period size: 59 Copynumber: 5.2 Consensus size: 56
1705 AAATCCTATT
* * *
1715 TTTTACCCCGAAACTTCCCAAAATTCCATTTTTAGCCCTG-AACTTCCAAAAATT-CCA
1 TTTTACCCC-AAA-TT-CCAAAAATCCATTTTTAACCCTGAAACTTCCCAAAATTACCA
* * * *
1772 TTTTTAGCCCCAAACTTCCAAAAATCTCATTTTTAACCTTAAAATTTCTCAAAATT-CCA
1 -TTTTA-CCCCAAA-TTCCAAAAATC-CATTTTTAACCCTGAAACTTCCCAAAATTACCA
* * *
1831 TTTTTAGCCCCGAACTTCCAAAAATCTCATTTTTGA-CCTCGAAACTTCCTAAAATTACCA
1 -TTTTA-CCCC-AAATTCCAAAAATC-CATTTTTAACCCT-GAAACTTCCCAAAATTACCA
** * * * * *
1891 TTTTACCCCCGGATGTCTAAAAACTCCATTTTTTA-CTTCGAAACTTCCTAAAATTACCC
1 TTTTA-CCCCAAAT-TCCAAAAA-TCCATTTTTAACCCT-GAAACTTCCCAAAATTACCA
* **
1950 TTTTACCCCTAAATGTCTAAAAATTCCATTTTTAACCCTGAATTTTCCCAAAATTACCA
1 TTTTACCCC-AAAT-TCCAAAAA-TCCATTTTTAACCCTGAAACTTCCCAAAATTACCA
*
2009 TTTCACCCC
1 TTTTACCCC
2018 CGAGAATCCA
Statistics
Matches: 203, Mismatches: 32, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
57 8 0.04
58 29 0.14
59 157 0.77
60 9 0.04
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (56 bp):
TTTTACCCCAAATTCCAAAAATCCATTTTTAACCCTGAAACTTCCCAAAATTACCA
Found at i:8107 original size:206 final size:206
Alignment explanation
Indices: 7844--8779 Score: 1311
Period size: 206 Copynumber: 4.6 Consensus size: 206
7834 GGACGTTTCT
* *
7844 AGATGAGATACTGAGGAGTGAACCAAATTTGCCTTCCTGATTAGATACAGAGAAGCGGATTGAAA
1 AGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
* * *
7909 TAAGCGATGCGGTCATCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCCATGCTCAAA
66 CAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCCACGCTCAAA
* * *
7974 GCGAGTAAAATCTTCGAACCCGAGCTTCTTGATGAGACACCGAGAAGCAGGTCGAAGCAGTAAAC
131 GCGAGTAAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAC
*
8039 GGTTAGTTTCC
196 GGTTAGCTTCC
8050 AGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
1 AGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
* * *
8115 CAAGCGATGCAGTCATCTTCCAGATGAGATACTGAGAAGAAGACCAAATTAAGCCCACGCTCAAA
66 CAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCCACGCTCAAA
* * * *
8180 GCGAGTAAAATCTTCGAACCCTAGCTTCTTGATGAGACACCGAGAAGTAGGTCGAAGCAGTAAAC
131 GCGAGTAAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAC
*
8245 AGTTAGCTTCC
196 GGTTAGCTTCC
* *
8256 AGATGAGATACTGAGGAGTGAACCAAATTCTCCTTCCTGATGAGATACAGAGAAGCGAATTGAAA
1 AGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
** * *
8321 CAAGCGATGCGGTCATCTTCCCAATGAGATACTAAAAAGAAGACCAAATCAAGCCCACGCTCAAA
66 CAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCCACGCTCAAA
*
8386 GCGAGTAAAATCTTCAAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAC
131 GCGAGTAAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAC
8451 GGTTAGCTTCC
196 GGTTAGCTTCC
* * *
8462 AAATGAGAAACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
1 AGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
** * * * * * *
8527 CAAGCGATGCGGTCATCTTTTTGATGAGATACTGAGGAGAAGACCAAACCAAACCCACACAC-GA
66 CAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCCACGCTCAAA
* * * * * * * *
8591 -TGAAT-AAACCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCTGGTCGAAGTAATAAAA
131 GCGAGTAAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAAT-AAA
* *
8654 CGGATAGCTCCC
195 CGGTTAGCTTCC
* * * * * *
8666 TGATGAGATACTGAGGAGTTAACCAAATTCGTCTTCCTGATGAGATGCAGAGAAACAGATTGAAA
1 AGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
* * * * * * * *
8731 CAAACGACGTGGTCATCTCCCTGATGAGACATTGAGGAGAAGTCCAAAT
66 CAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT
8780 TAAACCCATG
Statistics
Matches: 658, Mismatches: 71, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
203 47 0.07
204 113 0.17
205 1 0.00
206 497 0.76
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (206 bp):
AGATGAGATACTGAGGAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
CAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCCACGCTCAAA
GCGAGTAAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAC
GGTTAGCTTCC
Found at i:9153 original size:6 final size:6
Alignment explanation
Indices: 9135--9209 Score: 86
Period size: 6 Copynumber: 13.0 Consensus size: 6
9125 CTGGGCCTTT
*
9135 TTTAAA TTT-AA TTTAAA TTTGAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
9181 TTT-AA TTTAAA TTTAAA TTCAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
9210 AAGTCCAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
4 2 0.03
5 12 0.20
6 42 0.71
7 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:9162 original size:23 final size:23
Alignment explanation
Indices: 9135--9209 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
9125 CTGGGCCTTT
*
9135 TTTAAATTTAATTTAAATTTGAA
1 TTTAAATTTAATTTAAATTTAAA
9158 TTTAAA-TTAATCTTAAATTTAAA
1 TTTAAATTTAAT-TTAAATTTAAA
*
9181 TTT-AATTTAAATTTAAATTCAAA
1 TTTAAATTT-AATTTAAATTTAAA
*
9204 GTTAAA
1 TTTAAA
9210 AAGTCCAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.16
23 33 0.73
24 5 0.11
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (23 bp):
TTTAAATTTAATTTAAATTTAAA
Found at i:9197 original size:17 final size:17
Alignment explanation
Indices: 9135--9199 Score: 89
Period size: 17 Copynumber: 3.8 Consensus size: 17
9125 CTGGGCCTTT
9135 TTTAAATTT-AATTTAAA
1 TTTAAATTTAAATTT-AA
*
9152 TTTGAATTTAAA-TTAA
1 TTTAAATTTAAATTTAA
9168 TCTTAAATTTAAATTTAA
1 T-TTAAATTTAAATTTAA
9186 TTTAAATTTAAATT
1 TTTAAATTTAAATT
9200 CAAAGTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 3 0.07
17 33 0.77
18 7 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:9208 original size:12 final size:11
Alignment explanation
Indices: 9135--9209 Score: 71
Period size: 11 Copynumber: 6.5 Consensus size: 11
9125 CTGGGCCTTT
*
9135 TTTAAATTTAA
1 TTTAAATTAAA
*
9146 TTTAAATTTGAA
1 TTTAAA-TTAAA
9158 TTTAAATT-AA
1 TTTAAATTAAA
9168 TCTTAAATTTAAA
1 T-TTAAA-TTAAA
*
9181 TTTAATTTAAA
1 TTTAAATTAAA
9192 TTTAAATTCAAA
1 TTTAAATT-AAA
*
9204 GTTAAA
1 TTTAAA
9210 AAGTCCAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
10 3 0.05
11 25 0.45
12 24 0.44
13 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:9268 original size:15 final size:16
Alignment explanation
Indices: 9234--9270 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9224 AATTACATAA
9234 CCCAAATTACAAATGG
1 CCCAAATTACAAATGG
9250 CCCAAATT-CGAAA-GG
1 CCCAAATTAC-AAATGG
9265 CCCAAA
1 CCCAAA
9271 CTTTACACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.43, C:0.30, G:0.14, T:0.14
Consensus pattern (16 bp):
CCCAAATTACAAATGG
Done.