Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001651.1 Kokia drynarioides strain JFW-HI SEQ_113297, 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: 13745
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Found at i:194 original size:3 final size:3
Alignment explanation
Indices: 188--216 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
178 TTACCGTAAT
188 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
217 CAATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:926 original size:6 final size:6
Alignment explanation
Indices: 917--972 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
907 TTTGGACATT
* * * * *
917 AATTTA AATTTA AATTTA AACTTA AA-ATA AAATTA ATTTTA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
963 AATTTA AATT
1 AATTTA AATT
973 CTGTTGGGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 8 0.20
6 32 0.80
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:932 original size:12 final size:12
Alignment explanation
Indices: 917--972 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
907 TTTGGACATT
917 AATTTAAATTTA
1 AATTTAAATTTA
*
929 AATTTAAACTTA
1 AATTTAAATTTA
* *
941 AA-ATAAAATTA
1 AATTTAAATTTA
* *
952 ATTTTAAA-ATA
1 AATTTAAATTTA
963 AATTTAAATT
1 AATTTAAATT
973 CTGTTGGGCC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 17 0.50
12 17 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
AATTTAAATTTA
Found at i:947 original size:17 final size:17
Alignment explanation
Indices: 927--970 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
917 AATTTAAATT
927 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
* **
944 TAAAATTAATTTTAAAA
1 TAAATTTAAACTTAAAA
961 TAAATTTAAA
1 TAAATTTAAA
971 TTCTGTTGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:1734 original size:158 final size:158
Alignment explanation
Indices: 1443--1783 Score: 511
Period size: 158 Copynumber: 2.2 Consensus size: 158
1433 TTTCGACTTG
* *
1443 CTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTTACATCGAGCGTGGGTTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATT
* * * *
1508 TGGTCTTCTTCTCAATATCTCATCAGGAAGATAACCGTATTGCTTGTTTCAATCCGTTTCTCTGT
66 TGGTCTTCTTCTCAATATCTCATCAGGAAGATAACCGCATCGCTTGTTTCAATCCGCTTCTCTAT
*
1573 ATCTCATCAAGAAGATGGATTTGGTCCA
131 ATCTCATCAAGAAGATGAATTTGGTCCA
* * *
1601 CTTCTCAGTATCTCATGAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTGGGTTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATT
* * * * *
1666 TGGTTTTCTTCTCAGTATCTCATCAGGAAGGTGACCGCATCGCTTGTTTCAATCTGCTTCTCTAT
66 TGGTCTTCTTCTCAATATCTCATCAGGAAGATAACCGCATCGCTTGTTTCAATCCGCTTCTCTAT
* * *
1731 ATCTCATCAGGAAGATGAATTTGGTTCG
131 ATCTCATCAAGAAGATGAATTTGGTCCA
*
1759 CTTCTCAGTATCTCATCAAGAAGCT
1 CTTCTCAGTATCTCATCAGGAAGCT
1784 AACCTTTTTA
Statistics
Matches: 164, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
158 164 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (158 bp):
CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATT
TGGTCTTCTTCTCAATATCTCATCAGGAAGATAACCGCATCGCTTGTTTCAATCCGCTTCTCTAT
ATCTCATCAAGAAGATGAATTTGGTCCA
Found at i:1959 original size:206 final size:206
Alignment explanation
Indices: 1600--2068 Score: 778
Period size: 206 Copynumber: 2.3 Consensus size: 206
1590 GATTTGGTCC
* * *
1600 ACTTCTCAGTATCTCATGAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTGGGTTTGAT
1 ACTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTGCTCGCATTGAGCGTGAGTTTGAT
* *
1665 TTGGTTTTCTTCTCAGTATCTCATCAGGAAGGTGACCGCATCGCTTGTTTCAATCTGCTTCTCTA
66 TTGGTCTTCTTCTCAGTATCTCATCAAGAAGGTGACCGCATCGCTTGTTTCAATCTGCTTCTCTA
* *
1730 TATCTCATCAGGAAGATGAATTTGGTTCGCTTCTCAGTATCTCATCAAGAAGCTAACCTTTTTAT
131 TATCTCATCAGGAAGACGAATTTGGTTCGCTTCTCAGTATCTCATCAAGAAGCTAACCCTTTTAT
*
1795 TGCTTCTACCT
196 TGCTTCGACCT
* *
1806 GCTTCTCAGTATCTCATCAGAAAGCTGGAGTTCGAAGATTTGCTCGCATTGAGCGTGAGTTTGAT
1 ACTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTGCTCGCATTGAGCGTGAGTTTGAT
1871 TTGGTCTTCTTCTCAGTATCTCATCAAGAAGGTGACCGCATCGCTTGTTTCAAT-TCGCTTCTCT
66 TTGGTCTTCTTCTCAGTATCTCATCAAGAAGGTGACCGCATCGCTTGTTTCAATCT-GCTTCTCT
* *
1935 GTATCTCATCAGGAAGACGAATTTGGTTCGCTTCTCAGTATCTCATCAGGAAGCTAACCCTTTTA
130 ATATCTCATCAGGAAGACGAATTTGGTTCGCTTCTCAGTATCTCATCAAGAAGCTAACCCTTTTA
2000 TTGCTTCGACCT
195 TTGCTTCGACCT
* * **
2012 ACTTCTTAGTATCTCATCGGGAAGCTGGAGTTCGAAGATTTGCTCATATTGAGCGTG
1 ACTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTGCTCGCATTGAGCGTG
2069 GGTTCGAAGA
Statistics
Matches: 244, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
205 1 0.00
206 243 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (206 bp):
ACTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTGCTCGCATTGAGCGTGAGTTTGAT
TTGGTCTTCTTCTCAGTATCTCATCAAGAAGGTGACCGCATCGCTTGTTTCAATCTGCTTCTCTA
TATCTCATCAGGAAGACGAATTTGGTTCGCTTCTCAGTATCTCATCAAGAAGCTAACCCTTTTAT
TGCTTCGACCT
Found at i:1976 original size:364 final size:364
Alignment explanation
Indices: 1307--1989 Score: 952
Period size: 364 Copynumber: 1.9 Consensus size: 364
1297 TGACTTAGCC
** * *
1307 TTCTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTTGATCCACTTCTCTATGTTTC
1 TTCTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTCTATATCTC
* * * * * * * * * *
1372 ATTAGGAAGACGGATTTGGTTTACTTATCCGTTTTTCTTCAGGAAGCTAATCATTTTATTGTTTC
66 ATCAGGAAGACGAATTTGGTTCACTTATCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTC
* * * * * *
1437 GACTTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTTACATCGAGCGTGGGT
131 GACCTGCTTCTCAGTATCTCATCAGAAAGCTGGAGTTCGAAGATTTGCTCACATCGAGCGTGAGT
* * * *
1502 TTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATAACCGTATTGCTTGTTTCAATCCGTTT
196 TTGATTTGGTCTTCTTCTCAATATCTCATCAAGAAGATAACCGCATCGCTTGTTTCAATCCGCTT
* * *
1567 CTCTGTATCTCATCAAGAAGATGGATTTGGTCCACTTCTCAGTATCTCATGAGGAAGCTGGGGTT
261 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGGGGTT
1632 CGAAGATTTGCTCGCATTGAGCGTGGGTTTGATTTGGTT
326 CGAAGATTTGCTCGCATTGAGCGTGGGTTTGATTTGGTT
* * * **
1671 TTCTTCTCAGTATCTCATCAGGAAGGTGACCGCATCGCTTGTTTCAATCTGCTTCTCTATATCTC
1 TTCTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTCTATATCTC
* * * *
1736 ATCAGGAAGATGAATTTGGTTCGCTTCTCAGTATCTCATCAAGAAGCTAACCTTTTTATTGCTTC
66 ATCAGGAAGACGAATTTGGTTCACTTATCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTC
* * *
1801 TACCTGCTTCTCAGTATCTCATCAGAAAGCTGGAGTTCGAAGATTTGCTCGCATTGAGCGTGAGT
131 GACCTGCTTCTCAGTATCTCATCAGAAAGCTGGAGTTCGAAGATTTGCTCACATCGAGCGTGAGT
* * * *
1866 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGGTGACCGCATCGCTTGTTTCAATTCGCTT
196 TTGATTTGGTCTTCTTCTCAATATCTCATCAAGAAGATAACCGCATCGCTTGTTTCAATCCGCTT
* * *
1931 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCGCTTCTCAGTATCTCATCAGGAAGCT
261 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
1990 AACCCTTTTA
Statistics
Matches: 273, Mismatches: 46, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
364 273 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (364 bp):
TTCTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCACTTCTCTATATCTC
ATCAGGAAGACGAATTTGGTTCACTTATCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTC
GACCTGCTTCTCAGTATCTCATCAGAAAGCTGGAGTTCGAAGATTTGCTCACATCGAGCGTGAGT
TTGATTTGGTCTTCTTCTCAATATCTCATCAAGAAGATAACCGCATCGCTTGTTTCAATCCGCTT
CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGGGGTT
CGAAGATTTGCTCGCATTGAGCGTGGGTTTGATTTGGTT
Found at i:10695 original size:14 final size:14
Alignment explanation
Indices: 10676--10703 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10666 TGAGGAAGGG
10676 TTAGCACCCTCATA
1 TTAGCACCCTCATA
10690 TTAGCACCCTCATA
1 TTAGCACCCTCATA
10704 CGCCCAAAAT
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:0.36, G:0.07, T:0.29
Consensus pattern (14 bp):
TTAGCACCCTCATA
Found at i:11388 original size:28 final size:29
Alignment explanation
Indices: 11350--11410 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
11340 ATGAGACTTC
11350 TTGGATACTC-GGGGGTAAAATGATAATT
1 TTGGATACTCGGGGGGTAAAATGATAATT
* *
11378 TTGGATTCTCGGGGGGTAAAATGGTAATT
1 TTGGATACTCGGGGGGTAAAATGATAATT
11407 TTGG
1 TTGG
11411 GAAAGTTCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.34
Consensus pattern (29 bp):
TTGGATACTCGGGGGGTAAAATGATAATT
Found at i:11574 original size:29 final size:29
Alignment explanation
Indices: 11542--11879 Score: 227
Period size: 29 Copynumber: 11.8 Consensus size: 29
11532 ATTCGAGATC
*
11542 AAAAATGGAATTTTTGGACA-TTTGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTGAGGGT
* * * *
11571 -AAAAGGGTAATTTTTGAAAGTTTCGAAGTT
1 AAAAATGG-AATTTTTGGAAGTTT-GAGGGT
*
11601 AAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
*
11630 AAAAATGTAATTTTTGGAAGTTTCG-GGGT
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
*
11659 CAAAAATGGAATTTTTGGAAGTTTAAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGAGGGT
* *
11689 AAAAATGTAATTTTTAGAAGTTTCGA-GGT
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
* *
11718 CAAAATGGAATTTTTGGAAG-TTCAGGGAT
1 AAAAATGGAATTTTTGGAAGTTTGAGGG-T
* *
11747 AAAAATGTATTTTTTGG--G-TT-A----
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
* * * * *
11768 AAAAATGTAGTTTTTGGAAGTTCGTGGAT
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
* * * *
11797 AAAAATGTAATTTTTGGAAGTTCGTGGAT
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
** ***
11826 AAAAATATAATTTTCAAAAGTTTTG-GGGT
1 AAAAATGGAATTTTTGGAAG-TTTGAGGGT
*
11855 CAAAAATGGAATTATTGGATAGTTT
1 -AAAAATGGAATTTTTGGA-AGTTT
11880 AAGGACCTCA
Statistics
Matches: 248, Mismatches: 40, Indels: 41
0.75 0.12 0.12
Matches are distributed among these distances:
21 16 0.06
23 1 0.00
24 1 0.00
26 1 0.00
27 4 0.02
28 11 0.04
29 144 0.58
30 62 0.25
31 8 0.03
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:11596 original size:59 final size:58
Alignment explanation
Indices: 11475--11761 Score: 260
Period size: 59 Copynumber: 4.9 Consensus size: 58
11465 TTCAAAAAAA
* ** * * ** * *
11475 TCGAGACCAAAAACAGAATTTTTGGACA-ATCGGGGGTAAATTGGTAATTTTTAAGGAAT
1 TCGAGATCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAGGTAATTTTTAAAG-TT
* * *
11534 TCGAGATCAAAAATGGAATTTTTGGACA-TTTGGGGGTAAAAGGGTAATTTTTGAAAGTT
1 TCGAGATCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAGGTAATTTTT-AAAGTT
* * *
11593 TCGA-AGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTT
1 TCGAGA-TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAGGTAATTTTT-AAAGTT
* * ** *
11652 TCGGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTAGAAGTT
1 TCGAGATCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAGGTAATTTTTA-AAGTT
* * *
11711 TCGAGGTC-AAAATGGAATTTTTGGAAGTTC-AGGGATAAAAATGTATTTTTT
1 TCGAGATCAAAAATGGAATTTTTGGAAGTTCGAGGG-TAAAAAGGTAATTTTT
11762 GGGTTAAAAA
Statistics
Matches: 198, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
57 4 0.02
58 38 0.19
59 153 0.77
60 3 0.02
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (58 bp):
TCGAGATCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAGGTAATTTTTAAAGTT
Found at i:11736 original size:88 final size:86
Alignment explanation
Indices: 11520--11739 Score: 241
Period size: 88 Copynumber: 2.5 Consensus size: 86
11510 GTAAATTGGT
* *
11520 AATTTTTAAGGAA-TTCGAGATCAAAAATGGAATTTTTGGACA-TTTGGGGGTAAAAGGGTAATT
1 AATTTTT-A-GAAGTTCGAGGTC-AAAATGGAATTTTTGGA-AGTTTCGGGGTAAAAGGGTAATT
*
11583 TTTGAAAGTTTCGAAGTTAAAAATGG
62 TTTGAAAGTTTC-AAGGTAAAAATGG
* * * *
11609 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCGGGGTCAAAAATGG-AATTT
1 AATTTTTAGAAGTTCGA-GGTCAAAATGGAATTTTTGGAAGTTTCGGGGT--AAAAGGGTAATTT
* *
11673 TTGGAAGTTT-AAGGGTAAAAATGT
63 TTGAAAGTTTCAA-GGTAAAAATGG
11697 AATTTTTAGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAGTT
1 AATTTTTAGAAG-TTCGAGGTCAAAATGGAATTTTTGGAAGTT
11740 CAGGGATAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
87 6 0.05
88 72 0.64
89 28 0.25
90 6 0.05
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (86 bp):
AATTTTTAGAAGTTCGAGGTCAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAGGGTAATTTTTG
AAAGTTTCAAGGTAAAAATGG
Found at i:11797 original size:50 final size:50
Alignment explanation
Indices: 11719--11813 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
11709 TTTCGAGGTC
*
11719 AAAATGGAATTTTTGGAAGTTCAGGGATAAAAATGTATTTTTTGGGTTAA
1 AAAATGGAATTTTTGGAAGTTCAGGGATAAAAATGTAATTTTTGGGTTAA
* *
11769 AAAATGTAGTTTTTGGAAGTTC-GTGGATAAAAATGTAATTTTTGG
1 AAAATGGAATTTTTGGAAGTTCAG-GGATAAAAATGTAATTTTTGG
11814 AAGTTCGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 1 0.02
50 40 0.98
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (50 bp):
AAAATGGAATTTTTGGAAGTTCAGGGATAAAAATGTAATTTTTGGGTTAA
Done.