Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011099.1 Kokia drynarioides strain JFW-HI SEQ_126072, 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: 4313
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Found at i:2135 original size:205 final size:197
Alignment explanation
Indices: 1773--2285 Score: 744
Period size: 205 Copynumber: 2.6 Consensus size: 197
1763 ATAACAACGC
* * * *
1773 GGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACTCATGCTCGATGTGAGCAAAT
1 GGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAACAAAT
*
1838 CTTCGAATCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTGAGCTTCC
66 CTTCGAATCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTGAGCTTCC
* *
1903 TGATGAGATACTGAAAAGTAGACCAAATTCGTCTTCCTGATAAGTTACAGAGAAACAAATTGAAA
131 TGATGAGATACAGAAAAGGAGACCAAATTCGTCTT-C--AT-A--T--AGAGAAACAAATTGAAA
*
1968 TAAATGACGT
188 CAAATGACGT
*
1978 GGTCATCTTCTTGATGAGATACTAAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAACAAAT
1 GGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAACAAAT
2043 CTTCGAATCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTGAGCTTCC
66 CTTCGAATCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTGAGCTTCC
* *
2108 TGATGAGATACAGAGAAGCGA-ACCAAATTCGTCTTCATATAGAGAAGCAAATTGAAACAAATGA
131 TGATGAGATACAGAAAAG-GAGACCAAATTCGTCTTCATATAGAGAAACAAATTGAAACAAATGA
*
2172 TGT
195 CGT
* *
2175 GGTCATCTTCTAGATGAGATACTGAGAAAGAAGACCAAGTCAAACCCATGCTCGATGT-AAGCAA
1 GGTCATCTTCTTGATGAGATACTGAG-AAGAAGACCAAATCAAACCCATGCTCGATGTGAA-CAA
* * *
2239 ATCTTCGAATCCCAACTTTCTGA-GCAGAAACTGAGAAGCAGGTCGAA
64 ATCTTCGAATCCCAGCTTCCTGATG-AGACACTGAGAAGCAGGTCGAA
2286 CCAAATTCGT
Statistics
Matches: 286, Mismatches: 18, Indels: 15
0.90 0.06 0.05
Matches are distributed among these distances:
197 51 0.18
198 75 0.26
199 1 0.00
201 1 0.00
202 2 0.01
204 1 0.00
205 154 0.54
206 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (197 bp):
GGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAACAAAT
CTTCGAATCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTGAGCTTCC
TGATGAGATACAGAAAAGGAGACCAAATTCGTCTTCATATAGAGAAACAAATTGAAACAAATGAC
GT
Found at i:2772 original size:204 final size:204
Alignment explanation
Indices: 2338--2784 Score: 554
Period size: 204 Copynumber: 2.2 Consensus size: 204
2328 ACAAATGACG
* *
2338 TGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAGCAAA
1 TGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA-GTGAACAAA
** * * * *
2403 TCTTCGAGTCCCAACTTCTTGATGAGACACTGAGAGGCATGTCGAAGAAATAAACGGTTAGCTTC
65 TCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCAAAGAAATAAACGGTTAGCTTC
* * * * * * * * **
2468 CTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAATGGATTGAA
130 CTGATGAAATACGGAGAAGTAAACCAAAATCATCTTCCTGATAAAACACAGAGAAATGGATCAAA
*
2533 ACAAACAACG
195 ACAAACAACA
2543 TGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA-TGAACAAAT
1 TGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGAGTGAACAAAT
* ** * * * *
2607 CTTCTAACCCCAGTTTCCTGATGAGATACTGAGAAGCAGGTTAAAGTAATAAAACGGTTAGTTTC
66 CTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCAAAGAAAT-AAACGGTTAGCTTC
*
2672 CTGATGAAATACGGGGAAGTAAACCAAAATCATCTTCCTGATAAAACACAGAGAAATGGATCAAA
130 CTGATGAAATACGGAGAAGTAAACCAAAATCATCTTCCTGATAAAACACAGAGAAATGGATCAAA
* *** *
2737 ATAAGTGATA
195 ACAAACAACA
* * *
2747 TGGTCATCTTCCCGATGATATACTGAGAAGAAGGCCAA
1 TGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
2785 GTTAATGAAA
Statistics
Matches: 206, Mismatches: 35, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
203 46 0.22
204 106 0.51
205 54 0.26
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (204 bp):
TGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGAGTGAACAAAT
CTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCAAAGAAATAAACGGTTAGCTTCC
TGATGAAATACGGAGAAGTAAACCAAAATCATCTTCCTGATAAAACACAGAGAAATGGATCAAAA
CAAACAACA
Found at i:3199 original size:17 final size:17
Alignment explanation
Indices: 3177--3231 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
3167 AACTTTTTTT
3177 TTAAGTTTAAAATTAAA
1 TTAAGTTTAAAATTAAA
*
3194 TTAAGTTTAAAATTAAT
1 TTAAGTTTAAAATTAAA
*
3211 TTGAA-TTTAAAATTTAA
1 TT-AAGTTTAAAATTAAA
3228 TTAA
1 TTAA
3232 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 2 0.06
17 30 0.88
18 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
TTAAGTTTAAAATTAAA
Done.