Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012843.1 Kokia drynarioides strain JFW-HI SEQ_127856, 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: 15473
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:1554 original size:30 final size:29
Alignment explanation
Indices: 1460--1554 Score: 118
Period size: 29 Copynumber: 3.2 Consensus size: 29
1450 CTAAATTATT
* **
1460 CAAAAATCCCATTTTTACCCCCGAACTTC
1 CAAAAATCCCATTTTTACCTCAAAACTTC
*
1489 CAAAAATCCCATTTTTACCTCTAAACTTC
1 CAAAAATCCCATTTTTACCTCAAAACTTC
* *
1518 TAAAAATCCCATTTTTGACCTCAAAATTTC
1 CAAAAATCCCATTTTT-ACCTCAAAACTTC
*
1548 CCAAAAT
1 CAAAAAT
1555 TACCGTTTCG
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 41 0.72
30 16 0.28
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.32
Consensus pattern (29 bp):
CAAAAATCCCATTTTTACCTCAAAACTTC
Found at i:1621 original size:29 final size:29
Alignment explanation
Indices: 1566--1622 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1556 ACCGTTTCGT
*
1566 CCCCGAGAATCCAAAATTATCACTTTTGC
1 CCCCGAGAATCCAAAAATATCACTTTTGC
* *
1595 CCCCGGGAATCCGAAAAATCTCA-TTTTG
1 CCCCGAGAATCC-AAAAATATCACTTTTG
1623 AATTCCGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
CCCCGAGAATCCAAAAATATCACTTTTGC
Found at i:1998 original size:95 final size:95
Alignment explanation
Indices: 1827--2009 Score: 221
Period size: 95 Copynumber: 1.9 Consensus size: 95
1817 TTTTTTAAAA
* *
1827 AATCGAGACAATGTTTCCTTTACTTCGAGTTTCGAAAATTTGTGACTTAACTCACTAGGTGCATT
1 AATCGAGACAATGTTTCCTTTACTTCGAGTTTCGAAAATTTGCGACTTAACTCACTAGGTGCACT
*
1892 TTTTTCAAATCGAAATAATCGAACACCCTT
66 TTCTTCAAATCGAAATAATCGAACACCCTT
* * * *
1922 AATCGAGGCAATGTTTCC-TTATCTTCGA-TTAT-GAATA-TTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGACAATGTTTCCTTTA-CTTCGAGTT-TCGAAAATTTGCGACTTAACTCACTAGGTGC-
* *
1983 ACCTTTCTTCGAATCGAGATAATCGAA
63 A-CTTTCTTCAAATCGAAATAATCGAA
2010 TATCCTTTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
93 20 0.27
94 10 0.13
95 45 0.60
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (95 bp):
AATCGAGACAATGTTTCCTTTACTTCGAGTTTCGAAAATTTGCGACTTAACTCACTAGGTGCACT
TTCTTCAAATCGAAATAATCGAACACCCTT
Found at i:13739 original size:200 final size:200
Alignment explanation
Indices: 13392--13977 Score: 870
Period size: 200 Copynumber: 2.9 Consensus size: 200
13382 ACACGGTCAT
* *
13392 TCTCCCTGATGAGATACTGAGGAGAAGACCCAAACAAGGCTCAAAGCAAGCAAAATCTTCGAACC
1 TCTCCCTGATGAGATATTGAGGAGAAGAACCAAACAAGGCTCAAAGCAAGCAAAATCTTCGAACC
*
13457 CCAGCTTCATGATGAGACACTGAGAAGCGGGCTGAAGCAATAAATGGTTAGCTTCCTGATGAGAT
66 CCAGCTTCATGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCCTGATGAGAT
* *
13522 ACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGGTTGAAACGATGATAG
131 ACGGAGAAGTAAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACGATGATAG
13587 GAACA
196 GAACA
13592 TCTCCCTGATGAGATATTGAGGAGAAGAACCAAACAAGGCTCAAAGCAAGCAAAATCTTCGAACC
1 TCTCCCTGATGAGATATTGAGGAGAAGAACCAAACAAGGCTCAAAGCAAGCAAAATCTTCGAACC
* *
13657 CCAGCTTCTTGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCTTGATGAGAT
66 CCAGCTTCATGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCCTGATGAGAT
* *
13722 ACGGAGAAGTAAACCAAATTCGTCTTCCTGACGAGATACAGAGAAGCGGATTAAAACGATGATAG
131 ACGGAGAAGTAAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACGATGATAG
*
13787 GACCA
196 GAACA
* * * * ** * *
13792 TCTTCCTGATGAGACATTGAGGAGAAGATCCAAACGAGGCTCAAAGTGAGCCAAATCTTTTGAAC
1 TCTCCCTGATGAGATATTGAGGAGAAGAACCAAACAAGGCTCAAAGCAAGCAAAATC-TTCGAAC
* ** ** ** * *
13857 CCTAGCTTCCCGATGAGACACTGAGAAGTAGGTGGAAGC--CAAATGGTTAGCCTCCTGATGAGA
65 CCCAGCTTCATGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCCTGATGAGA
* * * *
13920 TATGGGGAAGTAAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGTGGATTGAAAC
130 TACGGAGAAGTAAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
13978 AAGTGATGCG
Statistics
Matches: 351, Mismatches: 34, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
199 73 0.21
200 240 0.68
201 38 0.11
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (200 bp):
TCTCCCTGATGAGATATTGAGGAGAAGAACCAAACAAGGCTCAAAGCAAGCAAAATCTTCGAACC
CCAGCTTCATGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCCTGATGAGAT
ACGGAGAAGTAAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACGATGATAG
GAACA
Done.