Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013668.1 Kokia drynarioides strain JFW-HI SEQ_128696, 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: 4476
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:433 original size:39 final size:38
Alignment explanation
Indices: 374--510 Score: 143
Period size: 39 Copynumber: 3.5 Consensus size: 38
364 GATAACTACA
374 ATCTGCCCCAAGCTCGGGGTAGGAGATTGGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTA-GAGATTGGTTGATGGTG
* * * * *
413 ATCTACCCCAAGCTCGGGGTAAAAAGTCG--GATGGTTG
1 ATCTGCCCCAAGCTCGGGGTAGAGATTGGTTGATGG-TG
* * *
450 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTAACGATG
1 --ATCTGCCCCAAGCTCGGGGT-AGAGATTGGTTGATGGTG
491 ATCTGCCCCAAGCTCGGGGT
1 ATCTGCCCCAAGCTCGGGGT
511 GAAAGAACAA
Statistics
Matches: 79, Mismatches: 13, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
36 5 0.06
37 2 0.03
38 4 0.05
39 59 0.75
40 5 0.06
41 2 0.03
42 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.23
Consensus pattern (38 bp):
ATCTGCCCCAAGCTCGGGGTAGAGATTGGTTGATGGTG
Found at i:501 original size:78 final size:76
Alignment explanation
Indices: 372--592 Score: 307
Period size: 78 Copynumber: 2.9 Consensus size: 76
362 TGGATAACTA
* * * *
372 CAATCTGCCCCAAGCTCGGGGTAGGAGATTGGTTGATGGTGATCTACCCCAAGCTCGGGGTAAAA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCCCAAGCTCGGGGTAAAA
**
437 AGTCGGATGGTTG
66 A--CAAATGGTTG
*
450 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTAACGATGATCTGCCCCAAGCTCGGGGTGAAA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCCCAAGCTCGGGGT-AAA
515 GAACAAATGGTTG
65 -AACAAATGGTTG
* * * *
528 CAATCTGCCCTAGGTTCGGGGTAAGAGATTGGTTGACGATGATTTGCCCCAAGCTCGGGGTAAAA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCCCAAGCTCGGGGTAAAA
593 GNNNNNNNNN
Statistics
Matches: 129, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
76 1 0.01
77 3 0.02
78 120 0.93
79 3 0.02
80 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (76 bp):
CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGACGATGATCTGCCCCAAGCTCGGGGTAAAA
ACAAATGGTTG
Found at i:534 original size:39 final size:38
Alignment explanation
Indices: 413--591 Score: 120
Period size: 39 Copynumber: 4.6 Consensus size: 38
403 GTTGATGGTG
* *
413 ATCTACCCCAAGCTCGGGGTAAA-AAGTCGGATGGTTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAGAA--CGAATGGTTGCA
* *
452 ATCTGCCCCAAGCTCGGGGT-AAG-A-GATTGGTTAACGA
1 ATCTGCCCCAAGCTCGGGGTAAAGAACGAATGGTT-GC-A
*
489 TGATCTGCCCCAAGCTCGGGGTGAAAGAACAAATGGTTGCA
1 --ATCTGCCCCAAGCTCGGGGT-AAAGAACGAATGGTTGCA
* * * *
530 ATCTGCCCTAGGTTCGGGGT-AAG-A-GATTGGTTGACGA
1 ATCTGCCCCAAGCTCGGGGTAAAGAACGAATGGTTG-C-A
*
567 TGATTTGCCCCAAGCTCGGGGTAAA
1 --ATCTGCCCCAAGCTCGGGGTAAA
592 AGNNNNNNNN
Statistics
Matches: 110, Mismatches: 16, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
35 13 0.12
36 3 0.03
37 5 0.05
38 3 0.03
39 72 0.65
40 2 0.02
41 4 0.04
42 2 0.02
43 6 0.05
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (38 bp):
ATCTGCCCCAAGCTCGGGGTAAAGAACGAATGGTTGCA
Found at i:1060 original size:78 final size:77
Alignment explanation
Indices: 923--1156 Score: 290
Period size: 78 Copynumber: 3.0 Consensus size: 77
913 GATAACTACA
** * *
923 ATCTGCCCCAAGCTCGGGGTAAA-AAGTCGGATGGTTGCAATCTGCCCCAAGCTCAGGGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAAGAA--CAAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAG
*
987 ATTGGTTAACGATG
64 ATTGGTTGACGATG
* * *
1001 ATCTGCCCCAAGCTCGGGGTGAAAGAACAAATGGTTGCAAGCTACCCCAGGTTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGT-AAAGAACAAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGA
1066 TTGGTTGACGATG
65 TTGGTTGACGATG
* * * * * * *
1079 ATTTGCCCCAAGCTCGGGGTAAAAGATCAAACGGTTGCAATTTGCCCTAGGCTCGGGGTAAAAAA
1 ATCTGCCCCAAGCTCGGGGT-AAAGAACAAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGA
1144 TTGGTTGACGATG
65 TTGGTTGACGATG
1157 TAACTCCATT
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
78 130 0.96
79 3 0.02
80 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (77 bp):
ATCTGCCCCAAGCTCGGGGTAAAGAACAAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGAT
TGGTTGACGATG
Found at i:1429 original size:49 final size:49
Alignment explanation
Indices: 1376--1847 Score: 278
Period size: 49 Copynumber: 9.7 Consensus size: 49
1366 TAAGGTACCG
* *
1376 GGTTCGGCATTGCGACTTAAACCTTTCCCTTCATGTC-TCTGAAGTACTA
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCTG-GGTACTA
** *
1425 GGTTCGTTATTGCGACTTAAACCTTTCCC-TCTGTGTCTTCAT-GGTACTA
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTC-ATGTCTTC-TGGGTACTA
* * * * * * * *
1474 GATCCGCCGTTACGGCTTAGATCC-TTCCCTT-GTGTCTTCAT-GGTA-TT
1 GGTTCGCCATTGCGACTTA-AACCTTTCCCTTCATGTCTTC-TGGGTACTA
* * * * * * * *
1521 GGATCCACCGTTACGGCTTAGATCTTTCCC-TCGTGTCTTC-GTGGTACT-
1 GG-TTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCTG-GGTACTA
* ** * * * *
1569 GGATCCGCTGTTGCGGCTTAGATCTTTCCCTTTTATG-CTTCTGAGGTACTA
1 GG-TTCGCCATTGCGACTTAAACCTTTCCC-TTCATGTCTTCTG-GGTACTA
* * *
1620 GGTTCACCATTGCGACTTAAACCTTTCCCTTCATGTCTTC-GCGGT-TTT
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCTG-GGTACTA
* * * * *
1668 GGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTT-TGAGGTACTA
1 GG-TTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCTG-GGTACTA
* * *
1718 GGTTCGCCATTGCGACTTAAACCTTTCCCTT-ATGTCATC-GTGATA-TT
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCTG-GGTACTA
* * * **
1765 GGATCCGCCATTCCGACTTAGATATTTCCCTTCATGTC-TCTGAGGTACTA
1 GG-TTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCTG-GGTACTA
1815 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCA
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCA
1848 AATCTTCATG
Statistics
Matches: 333, Mismatches: 66, Indels: 48
0.74 0.15 0.11
Matches are distributed among these distances:
47 7 0.02
48 115 0.35
49 162 0.49
50 46 0.14
51 3 0.01
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (49 bp):
GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCTGGGTACTA
Found at i:1516 original size:48 final size:48
Alignment explanation
Indices: 1447--1796 Score: 231
Period size: 48 Copynumber: 7.2 Consensus size: 48
1437 CGACTTAAAC
*
1447 CTTTCCCTCTGTGTCTTCATGGTACTAGATCCGCCGTTACGGCTTAGAT
1 CTTTCCCT-TGTGTCTTCATGGTACTGGATCCGCCGTTACGGCTTAGAT
* * *
1496 CCTTCCCTTGTGTCTTCATGGTATTGGATCCACCGTTACGGCTTAGAT
1 CTTTCCCTTGTGTCTTCATGGTACTGGATCCGCCGTTACGGCTTAGAT
* * * *
1544 CTTTCCCTCGTGTCTTCGTGGTACTGGATCCGCTGTTGCGGCTTAGAT
1 CTTTCCCTTGTGTCTTCATGGTACTGGATCCGCCGTTACGGCTTAGAT
* * * * * * * * *
1592 CTTTCCCTTTTATGCTTC-TGAGGTACTAGG-TTCACCATTGCGACTTAAAC
1 CTTTCCCTTGTGT-CTTCAT--GGTACT-GGATCCGCCGTTACGGCTTAGAT
* ** ** *
1642 CTTTCCCTTCATGTCTTCGCGGTTTTGGATCCGCCGTTGCGGCTTAGAT
1 CTTTCCCTT-GTGTCTTCATGGTACTGGATCCGCCGTTACGGCTTAGAT
* * * * * * * *
1691 CTTTCCCTTCATGTCTTTGA-GGTACTAGG-TTCGCCATTGCGACTTAAAC
1 CTTTCCCTT-GTGTC-TTCATGGTACT-GGATCCGCCGTTACGGCTTAGAT
* * * * * * * *
1740 CTTTCCCTTATGTCATCGTGATATTGGATCCGCCATTCCGACTTAGAT
1 CTTTCCCTTGTGTCTTCATGGTACTGGATCCGCCGTTACGGCTTAGAT
*
1788 ATTTCCCTT
1 CTTTCCCTT
1797 CATGTCTCTG
Statistics
Matches: 239, Mismatches: 51, Indels: 23
0.76 0.16 0.07
Matches are distributed among these distances:
47 3 0.01
48 124 0.52
49 72 0.30
50 36 0.15
51 4 0.02
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (48 bp):
CTTTCCCTTGTGTCTTCATGGTACTGGATCCGCCGTTACGGCTTAGAT
Found at i:1675 original size:195 final size:195
Alignment explanation
Indices: 1399--1847 Score: 521
Period size: 195 Copynumber: 2.3 Consensus size: 195
1389 GACTTAAACC
* ** *
1399 TTTCCCTTCATGTCTCTGAAGTACTAGGTTCGTTATTGCGACTTAAACCTTTCCC-TCTGTGTCT
1 TTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTC-ATGTCT
* * *
1463 TCATGGTACTAGATCCGCCGTTACGGCTTAGATCCTTCCCTT-GTGTC-TTCATGGTA-TTGGAT
65 TCACGGTACTAGATCCGCCGTTACGGCTTAGATCCTTCCCTTCATGTCTTTCA-GGTACTAGG-T
* * * * * * * ** * *
1525 CCACCGTTACGGCTTAGATCTTTCCCTCGTGTCTTCGTGGTACTGGATCCGCTGTTGCGGCTTAG
128 CCACCATTACGACTTAAACCTTTCCCTCATGTCATCGTGATACTGGATCCGCCATTCCGACTTAG
*
1590 ATC
193 ATA
* *
1593 TTTCCCTTTTATG-CTTCTGAGGTACTAGGTTCACCATTGCGACTTAAACCTTTCCCTTCATGTC
1 TTTCCC-TTCATGTC-TCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTC
* ** * * * * *
1657 TTCGCGGTTTTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTTGAGGTACTAGGTT
64 TTCACGGTACTAGATCCGCCGTTACGGCTTAGATCCTTCCCTTCATGTCTTTCAGGTACTAGGTC
* * * *
1722 CGCCATTGCGACTTAAACCTTTCCCTTATGTCATCGTGATATTGGATCCGCCATTCCGACTTAGA
129 CACCATTACGACTTAAACCTTTCCCTCATGTCATCGTGATACTGGATCCGCCATTCCGACTTAGA
1787 TA
194 TA
1789 TTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCA
1 TTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCA
1848 AATCTTCATG
Statistics
Matches: 213, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
194 7 0.03
195 131 0.62
196 69 0.32
197 6 0.03
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (195 bp):
TTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTT
CACGGTACTAGATCCGCCGTTACGGCTTAGATCCTTCCCTTCATGTCTTTCAGGTACTAGGTCCA
CCATTACGACTTAAACCTTTCCCTCATGTCATCGTGATACTGGATCCGCCATTCCGACTTAGATA
Found at i:1809 original size:97 final size:97
Alignment explanation
Indices: 1398--1845 Score: 508
Period size: 97 Copynumber: 4.6 Consensus size: 97
1388 CGACTTAAAC
* ** *
1398 CTTTCCCTTCATGTCTCTGAAGTACTAGGTTCGTTATTGCGACTTAAACCTTTCCCTCTGTGTCT
1 CTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCT-TATGTCT
* * *
1463 TCATGGTACTAGATCCGCCGTTACGGCTTAGAT
65 TCGTGGTACTGGATCCGCCGTTGCGGCTTAGAT
* * * * * * * * * * * **
1496 CCTTCCCTT-GTGTCT-TCATGGTA-TTGGATCCACCGTTACGGCTTAGATCTTTCCCTCGTGTC
1 CTTTCCCTTCATGTCTCTGA-GGTACTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTATGTC
*
1558 TTCGTGGTACTGGATCCGCTGTTGCGGCTTAGAT
64 TTCGTGGTACTGGATCCGCCGTTGCGGCTTAGAT
* *
1592 CTTTCCCTTTTATG-CTTCTGAGGTACTAGGTTCACCATTGCGACTTAAACCTTTCCCTTCATGT
1 CTTTCCC-TTCATGTC-TCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTT-ATGT
* **
1656 CTTCGCGGTTTTGGATCCGCCGTTGCGGCTTAGAT
63 CTTCGTGGTACTGGATCCGCCGTTGCGGCTTAGAT
* *
1691 CTTTCCCTTCATGTCTTTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTATGTCAT
1 CTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTATGTCTT
* * * * *
1756 CGTGATATTGGATCCGCCATTCCGACTTAGAT
66 CGTGGTACTGGATCCGCCGTTGCGGCTTAGAT
*
1788 ATTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
1 CTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
1846 CAAATCTTCA
Statistics
Matches: 294, Mismatches: 47, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
96 46 0.16
97 118 0.40
98 83 0.28
99 47 0.16
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (97 bp):
CTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTATGTCTT
CGTGGTACTGGATCCGCCGTTGCGGCTTAGAT
Done.