Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008618.1 Kokia drynarioides strain JFW-HI SEQ_123297, 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: 7422
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:389 original size:87 final size:85
Alignment explanation
Indices: 229--513 Score: 283
Period size: 87 Copynumber: 3.3 Consensus size: 85
219 TTTTGGATAC
* * * **
229 TTAGGGGCAAAATGATAATTTTTGGATGATT-G-GGGCAAAATGGTAATTTTTGGATGCTCGGGG
1 TTAGGGTCAAAATG-TAATTTTTGGATG-TTCGAGGGCAAAAT-GTAATTTTTGGAAGTTTAGGG
*
292 GCAAAATGGTAATTTTGAAAAGT
63 GTAAAATGGTAATTTTGAAAAGT
*
315 TTAGGGTCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAAATGTGATTTTTGGAAGTTTAGGGG
1 TTAGGGTCAAAAT-GTAATTTTTGGATGTTCGAGGGC-AAAATGTAATTTTTGGAAGTTTAGGGG
*
380 TAAAATGGTAATTTTTGGAAAGT
64 TAAAATGGTAA-TTTTGAAAAGT
* * * * *
403 TCATGGTCAAAATGTAA-GTTTGTGAAGTTC-AGGGTCAAAATGTAATTTTTAGAAAGTTTAGGG
1 TTAGGGTCAAAATGTAATTTTTG-GATGTTCGAGGG-CAAAATGTAATTTTT-GGAAGTTTAGGG
* **
466 GTCAAAAT-GTATTTTTTTTAAAGT
63 GT-AAAATGGTA-ATTTTGAAAAGT
490 TTGAGGGTCAAAATGTAATTTTTG
1 TT-AGGGTCAAAATGTAATTTTTG
514 AAATGTTTAG
Statistics
Matches: 167, Mismatches: 20, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
85 2 0.01
86 47 0.28
87 69 0.41
88 45 0.27
89 4 0.02
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (85 bp):
TTAGGGTCAAAATGTAATTTTTGGATGTTCGAGGGCAAAATGTAATTTTTGGAAGTTTAGGGGTA
AAATGGTAATTTTGAAAAGT
Found at i:399 original size:29 final size:30
Alignment explanation
Indices: 209--555 Score: 212
Period size: 29 Copynumber: 11.9 Consensus size: 30
199 TTTGAGGGTG
* *
209 AAATGGTACTTTTTGGATA-CTTAGGGG-CA
1 AAATGGTAATTTTTGGA-AGTTTAGGGGTCA
* * *
238 AAATGATAATTTTTGGATGATT-GGGG-CA
1 AAATGGTAATTTTTGGAAGTTTAGGGGTCA
* * * *
266 AAATGGTAATTTTTGGATG-CTCGGGGGCA
1 AAATGGTAATTTTTGGAAGTTTAGGGGTCA
*
295 AAATGGTAA-TTTTGAAAAGTTTA-GGGTCA
1 AAATGGTAATTTTTG-GAAGTTTAGGGGTCA
* *
324 AAATGGTAATTTTTGGATG-TTCGAGGG-CAA
1 AAATGGTAATTTTTGGAAGTTTAG-GGGTC-A
*
354 AAAT-GTGATTTTTGGAAGTTTAGGGGT-A
1 AAATGGTAATTTTTGGAAGTTTAGGGGTCA
* *
382 AAATGGTAATTTTTGGAAAGTTCA-TGGTCA
1 AAATGGTAATTTTTGG-AAGTTTAGGGGTCA
* *
412 AAAT-GTAA-GTTTGTGAAGTTCA-GGGTCA
1 AAATGGTAATTTTTG-GAAGTTTAGGGGTCA
*
440 AAAT-GTAATTTTTAGAAAGTTTAGGGGTCA
1 AAATGGTAATTTTT-GGAAGTTTAGGGGTCA
* **
470 AAAT-GTATTTTTTTTAAAGTTT-GAGGGTCA
1 AAATGGTA-ATTTTTGGAAGTTTAG-GGGTCA
* * *
500 AAAT-GTAATTTTTGAAATGTTTAGAGGTGA
1 AAATGGTAATTTTTGGAA-GTTTAGGGGTCA
* * *
530 AAA-CGTGATTTTTGGATAGTTCAGGG
1 AAATGGTAATTTTTGGA-AGTTTAGGG
556 ACCTTTTGGG
Statistics
Matches: 259, Mismatches: 35, Indels: 47
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.00
28 64 0.25
29 98 0.38
30 89 0.34
31 7 0.03
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.36
Consensus pattern (30 bp):
AAATGGTAATTTTTGGAAGTTTAGGGGTCA
Found at i:1870 original size:16 final size:16
Alignment explanation
Indices: 1851--1886 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1841 GGGTAACTAG
1851 GTTTAGGTGTAATTAA
1 GTTTAGGTGTAATTAA
*
1867 GTTTAGGTGTAATTAG
1 GTTTAGGTGTAATTAA
1883 GTTT
1 GTTT
1887 GGATTGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (16 bp):
GTTTAGGTGTAATTAA
Found at i:2014 original size:17 final size:17
Alignment explanation
Indices: 1992--2042 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
1982 AATTTTTAAT
1992 TTTAAATCCAAAATAAA
1 TTTAAATCCAAAATAAA
*
2009 TTTAAATTCAAAATAAA
1 TTTAAATCCAAAATAAA
2026 TTTAAA-CTCAAAATAAA
1 TTTAAATC-CAAAATAAA
2043 ACTAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (17 bp):
TTTAAATCCAAAATAAA
Found at i:2062 original size:7 final size:7
Alignment explanation
Indices: 2052--2076 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2042 AACTAAAAAT
2052 AATTTAA
1 AATTTAA
2059 AATTTAA
1 AATTTAA
2066 AATTTAA
1 AATTTAA
2073 AATT
1 AATT
2077 GGGTTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:3284 original size:210 final size:207
Alignment explanation
Indices: 2671--3319 Score: 944
Period size: 208 Copynumber: 3.1 Consensus size: 207
2661 CTCTCAGTTT
* *
2671 ACTTCTCT-TATCTCATTAAGAAGGTAACCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
*
2735 CAGGAAGTTGGGGTTCGAAGATTTGCTCACTTTGAGTCTAGTTTCATTGATTTGGTTACTTCTCA
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGT-TAGTTTCATTGATTTGGTTACTTCTCA
* * **
2800 GTATCTCATTAGGAAGACGACCGCTTCACTTGTTTTGATCTGCTTCTCTGTGTCTCATCAGGAAG
130 GTATCTCATTAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAG
*
2865 ATGAATCTGGTTC
195 ACGAATCTGGTTC
* ** *
2878 TCTTCTCTGTATCTCATCAAGAAGGTAACTACTTTATTGCTTCGACCTGCTTCTCAATATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* * *
2943 CAGG-AGCTGGGGTTCGAAGATTTGCTCACTTTGAGATTGGTTTCATTTATTTAGTCTACTTCTC
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAG-TTAGTTTCATTGATTTGGT-TACTTCTC
3007 AGTATCTCATTAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAA
129 AGTATCTCATTAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAA
*
3072 GACGGATCTGGTTC
194 GACGAATCTGGTTC
* *
3086 ACTTCTCTGTATCTCATCATGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* * *
3151 CAGGAAGCTGGGGTTCGAAGTTTTGCTCACATCGAGCTGTAGTTTCATTGATTTGGTGTACTTCT
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAG-T-TAGTTTCATTGATTTGGT-TACTTCT
* * * * * * *
3216 TAGTATCTCATCAGAAAGATGATCGCATCATTTGTTTTGATCCACTTCTTTGTATCTCATCAGGA
128 CAGTATCTCATTAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGA
*
3281 AGACGAAT-TAGGTCC
193 AGACGAATCT-GGTTC
*
3296 ACTTCTCTGTATCTCATCAGGAAG
1 ACTTCTCTGTATCTCATCAAGAAG
3320 ATGACTACTT
Statistics
Matches: 396, Mismatches: 40, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
207 52 0.13
208 200 0.51
209 30 0.08
210 114 0.29
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (207 bp):
ACTTCTCTGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGTTAGTTTCATTGATTTGGTTACTTCTCAG
TATCTCATTAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGA
CGAATCTGGTTC
Found at i:3398 original size:39 final size:39
Alignment explanation
Indices: 3350--3541 Score: 129
Period size: 39 Copynumber: 4.9 Consensus size: 39
3340 GATAACTGCA
* * *
3350 ATCTGCCCCATAATCGAGGTAAGAGATTGGATGGCTATG
1 ATCTACCCCATGATCGAGGTAAGAGATCGGATGGCTATG
* * * *
3389 ATCTACCCCATGATCGGGGTAAGAGATCGGGTGACTGTG
1 ATCTACCCCATGATCGAGGTAAGAGATCGGATGGCTATG
* * * **
3428 ATCTACCTCATGAT-GAGGGTAAAAGATCGGATGGTTACA
1 ATCTACCCCATGATCGA-GGTAAGAGATCGGATGGCTATG
* * * * * * *
3467 ATCTGCCCCTATCA-CGAAGTAAGAGATTGGCT-GATAGTC
1 ATCTACCCC-ATGATCGAGGTAAGAGATCGGATGGCTA-TG
* * * *
3506 AACTACCCCAAGCTCGAGGTAAAAGATCGGATGGCT
1 ATCTACCCCATGATCGAGGTAAGAGATCGGATGGCT
3542 GGGATTTGCC
Statistics
Matches: 111, Mismatches: 36, Indels: 11
0.70 0.23 0.07
Matches are distributed among these distances:
38 5 0.05
39 99 0.89
40 7 0.06
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23
Consensus pattern (39 bp):
ATCTACCCCATGATCGAGGTAAGAGATCGGATGGCTATG
Found at i:3605 original size:39 final size:39
Alignment explanation
Indices: 3562--3657 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 39
3552 CCAGACTTAA
* *
3562 GGTAAAAGATCAGATGA-G-TGCATTCTGCCCCAGGCTCGG
1 GGTAAAAGATCGGATGACGATG-A-TCTGCCCCAAGCTCGG
* *
3601 GGTAAGAGATCGGTTGACGATGATCTGCCCCAAGCTCGG
1 GGTAAAAGATCGGATGACGATGATCTGCCCCAAGCTCGG
3640 GGTAAAAGATCGGATGAC
1 GGTAAAAGATCGGATGAC
3658 TGGGGTCTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 45 0.92
40 2 0.04
41 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.32, T:0.20
Consensus pattern (39 bp):
GGTAAAAGATCGGATGACGATGATCTGCCCCAAGCTCGG
Found at i:5664 original size:39 final size:39
Alignment explanation
Indices: 5621--5700 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
5611 TTTATTGAAA
*
5621 TAAAAGATAGTGGTCATGTGCCCTTTATGAAAGGATTCC
1 TAAAAGATAGTGGTCATGTGCCCTTTATAAAAGGATTCC
*
5660 TAAAAGATTGTGGTCATGTGCCCTTTATAAAAGGATTCC
1 TAAAAGATAGTGGTCATGTGCCCTTTATAAAAGGATTCC
5699 TA
1 TA
5701 TTACTCTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (39 bp):
TAAAAGATAGTGGTCATGTGCCCTTTATAAAAGGATTCC
Done.