Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010369.1 Kokia drynarioides strain JFW-HI SEQ_125242, 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: 14048
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:1139 original size:29 final size:29
Alignment explanation
Indices: 1095--1195 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 29
1085 TTAAGCTATC
**
1095 CAAAAATTATATTTTGACCCTAAACTTCT
1 CAAAAATTCCATTTTGACCCTAAACTTCT
** * *
1124 TTAAAATTCCATTTTGA-CCTAAAATTTCC
1 CAAAAATTCCATTTTGACCCT-AAACTTCT
*
1153 CAAAAATTACATTTT-ACCCCTAAACTT-T
1 CAAAAATTCCATTTTGA-CCCTAAACTTCT
1181 CAAAAATTCCATTTT
1 CAAAAATTCCATTTT
1196 AAACCTTGAT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
28 18 0.32
29 36 0.63
30 3 0.05
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.39
Consensus pattern (29 bp):
CAAAAATTCCATTTTGACCCTAAACTTCT
Found at i:1157 original size:28 final size:28
Alignment explanation
Indices: 1126--1196 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
1116 AAACTTCTTT
*
1126 AAAATTCCATTTTGA-CCTAAAATTTCCCA
1 AAAATTCCATTTT-ACCCTAAAATTT-CAA
* *
1155 AAAATTACATTTTACCCCTAAACTTTC-A
1 AAAATTCCATTTTA-CCCTAAAATTTCAA
1183 AAAATTCCATTTTA
1 AAAATTCCATTTTA
1197 AACCTTGATC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 15 0.41
29 13 0.35
30 9 0.24
ACGTcount: A:0.39, C:0.23, G:0.01, T:0.37
Consensus pattern (28 bp):
AAAATTCCATTTTACCCTAAAATTTCAA
Found at i:1252 original size:29 final size:29
Alignment explanation
Indices: 1112--1290 Score: 107
Period size: 30 Copynumber: 6.1 Consensus size: 29
1102 TATATTTTGA
** *
1112 CCCTAAACTTCTTTAAAATTCCATTTTGA-
1 CCCTAAACTT-TCCAAAATTCCATTTTTAC
* *
1141 -CCTAAAATTTCCCAAAAATTACA-TTTTAC
1 CCCTAAACTTT-CC-AAAATTCCATTTTTAC
* * *
1170 CCCTAAACTTTCAAAAATTCCATTTTAAA
1 CCCTAAACTTTCCAAAATTCCATTTTTAC
* * * * *
1199 CCTTGATCTTTTCATAAATTACATTTTTAC
1 CCCTAAACTTTCCA-AAATTCCATTTTTAC
**
1229 CCCCGAACTTTCCAAAATTCCATTTTTTAAC
1 CCCTAAACTTTCCAAAATTCCA-TTTTT-AC
* *
1260 CCCAAAAC-TTCTAAAATTACCA-TTTTAC
1 CCCTAAACTTTCCAAAATT-CCATTTTTAC
1288 CCC
1 CCC
1291 ATATATCTAA
Statistics
Matches: 115, Mismatches: 26, Indels: 19
0.72 0.16 0.12
Matches are distributed among these distances:
27 1 0.01
28 25 0.22
29 33 0.29
30 45 0.39
31 11 0.10
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAATTCCATTTTTAC
Found at i:1422 original size:29 final size:29
Alignment explanation
Indices: 1390--1467 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
1380 CGAACCTTCC
1390 AAAATTACCATTTTACCCCCAAACTTTCA
1 AAAATTACCATTTTACCCCCAAACTTTCA
* * * *
1419 AAAATT-CCATTTTGAACTCGAAACTTTCG
1 AAAATTACCATTTT-ACCCCCAAACTTTCA
*
1448 AAAATTATCATTTTACCCCC
1 AAAATTACCATTTTACCCCC
1468 GGATGTCTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 7 0.18
29 26 0.67
30 6 0.15
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAACTTTCA
Found at i:1521 original size:29 final size:29
Alignment explanation
Indices: 1488--1637 Score: 89
Period size: 29 Copynumber: 5.1 Consensus size: 29
1478 AGACTCCGTT
*
1488 TTTTATCTCGAACCTTCCAAAATTTACCA
1 TTTTATCTCGAACCTTCCAAAAATTACCA
* * * *
1517 TTTTACCCCCGAA--TGTCTAAAAACT-CCA
1 TTTTA-TCTCGAACCT-TCCAAAAATTACCA
1545 TTTTTGATCTCGAACCTTCCAAAAATTACCA
1 -TTTT-ATCTCGAACCTTCCAAAAATTACCA
* * *
1576 TTTTACCCCTGGA--TGTCCAAAAATT-CCA
1 TTTTATCTC-GAACCT-TCCAAAAATTACCA
*
1604 TTTTTGACCTC-AAGCCTTCCAAAAATTACCA
1 -TTTT-ATCTCGAA-CCTTCCAAAAATTACCA
1635 TTT
1 TTT
1638 CATCCCTGAG
Statistics
Matches: 92, Mismatches: 14, Indels: 29
0.68 0.10 0.21
Matches are distributed among these distances:
28 9 0.10
29 38 0.41
30 37 0.40
31 8 0.09
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.35
Consensus pattern (29 bp):
TTTTATCTCGAACCTTCCAAAAATTACCA
Found at i:1532 original size:175 final size:177
Alignment explanation
Indices: 1214--1637 Score: 538
Period size: 175 Copynumber: 2.4 Consensus size: 177
1204 ATCTTTTCAT
* * * *
1214 AAATTA-CATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTTAACCCCAAAACTTCTAAAATT
1 AAATTACCA-TTTTACCCCCAAACTTTCAAAAATTCCATTTTTGAACCCCAAAACTTCGAAAATT
*
1278 ACCATTTTACCCCATATATCTAAAAACTCAGTTTTTTTTATCTCAAACCTTCCAAAATTTACCAT
65 ACCATTTTACCCCAGATATCTAAAAACTCAG-TTTTTTTATCTCAAACCTTCCAAAATTTACCAT
*
1343 TTTACCCTCGAATGTCTAAAAACTCCATTTTTGATCCCGAACCTTCC-A
129 TTTACCCCCGAATGTCTAAAAACTCCATTTTTGATCCCGAACCTTCCAA
* *
1391 AAATTACCATTTTACCCCCAAACTTTCAAAAATTCCA-TTTTGAA-CTCGAAACTTTCGAAAATT
1 AAATTACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTGAACCCCAAAAC-TTCGAAAATT
* * * * * *
1454 ATCATTTTACCCCCGGATGTCTAAAGACTCCG-TTTTTTATCTCGAACCTTCCAAAATTTACCAT
65 ACCATTTTA-CCCCAGATATCTAAAAACTCAGTTTTTTTATCTCAAACCTTCCAAAATTTACCAT
*
1518 TTTACCCCCGAATGTCTAAAAACTCCATTTTTGATCTCGAACCTTCCAA
129 TTTACCCCCGAATGTCTAAAAACTCCATTTTTGATCCCGAACCTTCCAA
*** * * ** *
1567 AAATTACCATTTTACCCCTGGA-TGTCCAAAAATTCCATTTTTG-ACCTCAAGCCTTCCAAAAAT
1 AAATTACCATTTTACCCCCAAACT-TTCAAAAATTCCATTTTTGAACCCCAAAACTT-CGAAAAT
1630 TACCATTT
64 TACCATTT
1638 CATCCCTGAG
Statistics
Matches: 215, Mismatches: 24, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
175 83 0.39
176 58 0.27
177 72 0.33
178 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (177 bp):
AAATTACCATTTTACCCCCAAACTTTCAAAAATTCCATTTTTGAACCCCAAAACTTCGAAAATTA
CCATTTTACCCCAGATATCTAAAAACTCAGTTTTTTTATCTCAAACCTTCCAAAATTTACCATTT
TACCCCCGAATGTCTAAAAACTCCATTTTTGATCCCGAACCTTCCAA
Found at i:1627 original size:30 final size:31
Alignment explanation
Indices: 1542--1637 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
1532 TCTAAAAACT
*
1542 CCATTTTTGATCTCGAA-CCTTCCAAAAATTA
1 CCATTTTTGACCTC-AAGCCTTCCAAAAATTA
** **
1573 CCA-TTTT-ACC-CCTGGATGTCCAAAAATT-
1 CCATTTTTGACCTCAAGCCT-TCCAAAAATTA
1601 CCATTTTTGACCTCAAGCCTTCCAAAAATTA
1 CCATTTTTGACCTCAAGCCTTCCAAAAATTA
1632 CCATTT
1 CCATTT
1638 CATCCCTGAG
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 5 0.10
29 16 0.32
30 17 0.34
31 12 0.24
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.34
Consensus pattern (31 bp):
CCATTTTTGACCTCAAGCCTTCCAAAAATTA
Found at i:1645 original size:59 final size:59
Alignment explanation
Indices: 1152--1656 Score: 370
Period size: 59 Copynumber: 8.6 Consensus size: 59
1142 CTAAAATTTC
** * * ** * * *
1152 CCAAAAATTA-CATTTTACCCCTAAACT-TTCAAAAATTCCATTTTAAACCTTGATCTTT
1 CCAAAAATTACCATTTTACCCCCGAA-TGTCCAAAAACTCCATTTTTGACCTCGAACCTT
* * * * * * * *
1210 TCATAAATTA-CATTTTTACCCCCGAACTTTCC-AAAATTCCATTTTTTAACCCCAAAACTT
1 CCAAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAACTCCA-TTTTTGACCTCGAACCTT
* * * * * *
1270 -CTAAAATTACCATTTTA-CCCC-ATATATCTAAAAACT-CAGTTTTTTTTATCTCAAACCTT
1 CCAAAAATTACCATTTTACCCCCGA-ATGTCCAAAAACTCCA---TTTTTGACCTCGAACCTT
* * *
1329 CCAAAATTTACCATTTTACCCTCGAATGTCTAAAAACTCCATTTTTGATCC-CGAACCTT
1 CCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGA-CCTCGAACCTT
* * * * *
1388 CC-AAAATTACCATTTTACCCCCAAACT-TTCAAAAATTCCA-TTTTGAACTCGAAACTT
1 CCAAAAATTACCATTTTACCCCCGAA-TGTCCAAAAACTCCATTTTTGACCTCGAACCTT
* * * * * * * * *
1445 TCGAAAATTATCATTTTACCCCCGGATGTCTAAAGACTCCGTTTTTTATCTCGAACCTT
1 CCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCTCGAACCTT
* * *
1504 CCAAAATTTACCATTTTACCCCCGAATGTCTAAAAACTCCATTTTTGATCTCGAACCTT
1 CCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCTCGAACCTT
* * *
1563 CCAAAAATTACCATTTTACCCCTGGATGTCCAAAAATTCCATTTTTGACCTC-AAGCCTT
1 CCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCTCGAA-CCTT
* * * *
1622 CCAAAAATTACCATTTCATCCCTGAGTGTCCAAAA
1 CCAAAAATTACCATTTTACCCCCGAATGTCCAAAA
1657 TTACCGTTTT
Statistics
Matches: 362, Mismatches: 66, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
56 1 0.00
57 21 0.06
58 80 0.22
59 211 0.58
60 31 0.09
61 15 0.04
62 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCTCGAACCTT
Found at i:1654 original size:29 final size:29
Alignment explanation
Indices: 1562--1661 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 29
1552 TCTCGAACCT
* *
1562 TCCAAAAATTACCATTTTACCCCTG-GATG
1 TCCAAAAATTACCA-TTTATCCCTGAGCTG
* * *
1591 TCCAAAAATT-CCATTTTTGACCTCAAGCCT-
1 TCCAAAAATTACCATTTAT-CCCT-GAG-CTG
1621 TCCAAAAATTACCATTTCATCCCTGAG-TG
1 TCCAAAAATTACCATTT-ATCCCTGAGCTG
1650 TCC-AAAATTACC
1 TCCAAAAATTACC
1662 GTTTTACCCC
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
27 3 0.05
28 16 0.29
29 13 0.23
30 13 0.23
31 10 0.18
32 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.31
Consensus pattern (29 bp):
TCCAAAAATTACCATTTATCCCTGAGCTG
Found at i:3568 original size:16 final size:15
Alignment explanation
Indices: 3547--3576 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3537 TTAAATCGGT
3547 TTCGATTGAGTATTAG
1 TTCGATTGA-TATTAG
3563 TTCGATTGATATTA
1 TTCGATTGATATTA
3577 ATTTTATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
TTCGATTGATATTAG
Found at i:6250 original size:13 final size:12
Alignment explanation
Indices: 6232--6259 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6222 AAATTGATTG
6232 TTTTTTTTTTTC
1 TTTTTTTTTTTC
6244 TTTTTTTTTTTC
1 TTTTTTTTTTTC
6256 TTTT
1 TTTT
6260 GTCTAGCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:9663 original size:16 final size:18
Alignment explanation
Indices: 9630--9667 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
9620 TAAATATTAA
9630 ATTTATATATAAAGTTTG
1 ATTTATATATAAAGTTTG
*
9648 ATTTATAT-T-AATTTTG
1 ATTTATATATAAAGTTTG
9664 ATTT
1 ATTT
9668 GGTTCAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
ATTTATATATAAAGTTTG
Done.