Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011556.1 Kokia drynarioides strain JFW-HI SEQ_126545, 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: 2254
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Found at i:186 original size:62 final size:62
Alignment explanation
Indices: 41--214 Score: 204
Period size: 62 Copynumber: 2.8 Consensus size: 62
31 AAGTTTAGAT
* **
41 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACATAAAATAAGTTTTTGACAAGCTCGGAA
1 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGT-AAATAAGTTTTTGACAAGCTCAAAA
* ** * * * *
104 GTTCATCCAAGAACTGAGAGAGAAACAATACTTACGTGAATAAGTTTTTGTCAAGTTCAAAA
1 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTGACAAGCTCAAAA
* * * * *
166 GTTCGTCCGAGATCCAAGAGAGAACCAATTCTCATGTAAATAAGTTTTT
1 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTT
215 AATTCAGCGA
Statistics
Matches: 91, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
62 59 0.65
63 32 0.35
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (62 bp):
GTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTGACAAGCTCAAAA
Found at i:438 original size:62 final size:62
Alignment explanation
Indices: 356--525 Score: 218
Period size: 62 Copynumber: 2.7 Consensus size: 62
346 AAGTACGGAT
* *
356 GTTCATCCAAGAA-CGAAGAGAGAAACAATTC-AAGCGTAAATAAGTTTTTGACAAGTTTGGAA
1 GTTCATCCAAGAACCG-AGAGAGAAACAATTCTAA-CGTAAATAAGTTTTTGACAAGTTCGAAA
* *
418 GTTCATCCAAGAACCGAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGATAAGTTCGAAA
1 GTTCATCCAAGAACCGAGAGAGAAACAATTCTAACGTAAATAAGTTTTTGACAAGTTCGAAA
* * * * * *
480 GTTCGTCCATGAACCAAGAGAGAAATAATTCTCACGTAACTAAGTT
1 GTTCATCCAAGAACCGAGAGAGAAACAATTCTAACGTAAATAAGTT
526 AAATATCAAC
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
62 94 0.97
63 3 0.03
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (62 bp):
GTTCATCCAAGAACCGAGAGAGAAACAATTCTAACGTAAATAAGTTTTTGACAAGTTCGAAA
Found at i:842 original size:215 final size:217
Alignment explanation
Indices: 470--958 Score: 725
Period size: 215 Copynumber: 2.3 Consensus size: 217
460 AGTTTTTGAT
* *
470 AAGTTCGAAAGTTCGTCCATGAACCAAGAGAGAAATAATTCTCACGTAACTAAG-TTAAATATCA
1 AAGTTCGAAAGTTCGTCCATGAACCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTAATATCA
* * * * *
534 ACAGTCCAAAAGTTGTTTACAAAATGACAAACTATTTTGACCAAATGGTGTGATTTCTCGAGCAT
66 ACAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGGGATTTCTCGAGCAT
599 GGATTGTTCGAAAAATTTCTAGAAGGAATGGATTATCTTGATTACTTTTTGGAAACAAAGTTATA
131 GGATTGTTCGAAAAATTTCTAGAAGGAATGGATTATCTTGATTACTTTTTGGAAACAAAGTTATA
** * **
664 AAAGAGCTCGTGAAAGTTCGTC
196 AAAGAAATCGTAAAAGTTCGAA
* * * *
686 AAGTTCGAAAGTTCGTCCATTAACCAAGAGTGAAACAATTCTCACGTAAATAAGTTTTAATGT-A
1 AAGTTCGAAAGTTCGTCCATGAACCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTAATATCA
*
750 A-AGACCAAAACTTGTTTACAAAATGATAAACTATTTAGACCAAATGATGGGATTT-TCCGAGCA
66 ACAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGGGATTTCT-CGAGCA
813 TGGATTGTTCGAAAAATTTCTAGAAGGAATGGATTATCTTGATTACTTTTTGGAAACAAAGTTAT
130 TGGATTGTTCGAAAAATTTCTAGAAGGAATGGATTATCTTGATTACTTTTTGGAAACAAAGTTAT
*
878 AAAAGAAATCGTAAAAGTTTGAA
195 AAAAGAAATCGTAAAAGTTCGAA
* * * * **
901 AAGTTTGGATGTTCGTCCAAGAACCAAGAGAGAAATAATTCTTTCGTAAATAAGTTTT
1 AAGTTCGAAAGTTCGTCCATGAACCAAGAGAGAAATAATTCTCACGTAAATAAGTTTT
959 TGACAAGTTC
Statistics
Matches: 244, Mismatches: 27, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
214 1 0.00
215 185 0.76
216 52 0.21
217 6 0.02
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (217 bp):
AAGTTCGAAAGTTCGTCCATGAACCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTAATATCA
ACAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGGGATTTCTCGAGCAT
GGATTGTTCGAAAAATTTCTAGAAGGAATGGATTATCTTGATTACTTTTTGGAAACAAAGTTATA
AAAGAAATCGTAAAAGTTCGAA
Found at i:1011 original size:62 final size:62
Alignment explanation
Indices: 895--1021 Score: 137
Period size: 62 Copynumber: 2.0 Consensus size: 62
885 ATCGTAAAAG
* * * * ***
895 TTTGAAAAGTTTGGATGTTCGTCCAAGAACCAAGAGAGAAATAATTCTTTCGTAAATAAGTT
1 TTTGAAAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCACACGTAAATAAGTT
* ** * * *
957 TTTGACAAGTTCGGAAGTTCATCCAAGAACCAATTGGGAAACAATTCACACGTAACTATGTT
1 TTTGAAAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCACACGTAAATAAGTT
1019 TTT
1 TTT
1022 AATTTGCAGT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (62 bp):
TTTGAAAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCACACGTAAATAAGTT
Found at i:1850 original size:215 final size:213
Alignment explanation
Indices: 957--1878 Score: 911
Period size: 215 Copynumber: 4.3 Consensus size: 213
947 TAAATAAGTT
* * ** * * * *
957 TTTGACAAGTTCGGAAGTTCATCCAAGAACCAATTGGGAAACAATTCACACGTAACTATGTTTTT
1 TTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
*** * * * * *
1022 AATTTGCAGTCCAACACT-TGTTTACAAAATGATAAACTATTTTGACCAAATGATGTTATTTCTC
66 AATTCAAAGACCAA-AATATGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTT-T-
* * **
1086 GAGCATGGAATGTTTGGAAAAATTGCTCGATTGAATGGATCGTCTTGAATACTTTAAGGAACCGA
128 GAGCAAGGAATG-TTCGAAAAA-TGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGA
*
1151 AGTTATAAAAGAAATCGCAAAAG
191 AGTTATAAAAGAAATCGTAAAAG
* * *
1174 TTTGACAAGTTCGGATA-TTCGT-------CCAAGAGAGAAACAATTCTTATGTAAATAAGTTTT
1 TTTGACAAGTTCAGA-AGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* * * * * *
1231 TAATTCAAA-ACCAAAACATGTTTACGAAATGATAAACTTTTTAGACCATACGATGTGATTTTAC
65 TAATTCAAAGACCAAAATATGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTT--
* * * * * * *
1295 GAG-AATGGAATGTTCAAAAAATTCTCAAAGGAATGGATCTTCTTGAATACTTTATGGTACTGAA
128 GAGCAA-GGAATGTTCGAAAAATGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAA
*
1359 GTTATAAAAGAACTCGTAAAAG
192 GTTATAAAAGAAATCGTAAAAG
* * * * * *
1381 TTTAAAAAGTTCAGAAATTCATCCAAGAACCAAGAGAGAAATAATTCTCATGTAAATAAGTTTTT
1 TTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * *
1446 AATTGAAAGACC-AAATCCTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAATTCTT
66 AATTCAAAGACCAAAAT-ATGTTTACAAAATGACAAACTATTTAGACCAAATGATGTG-ATT-TT
* * * *
1510 GAGCATGGAAATCTTCGAAAAACTGCCCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGA
128 GAGCAAGG-AATGTTCGAAAAA-TGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGA
* * *
1575 AGTTAAAAAACAACTCGTAAAAG
191 AGTTATAAAAGAAATCGTAAAAG
* * * * ** *
1598 TTT-AAAATGTTC-GAAAGTTTGTCTAAGAACAAAGAGAGAAACTGTTCTCACGTAAATATGTTT
1 TTTGACAA-GTTCAG-AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT
* *
1661 TTAATTCAAAGACCAAAATAT-TTTTCAAAATGACAAACTATTTAGACCAAATAATGTGATTTTC
64 TTAATTCAAAGACCAAAATATGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTT-
* * * * * *
1725 AGAGCAAGTAATGTTTGGAAAATAGCTCGAAGGAATGGATCATCATGAATACTTTCAGGAACCGA
128 -GAGCAAGGAATGTTCGAAAAAT-GCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGA
1790 AGTTATAAAAGAAATCGTAAAAG
191 AGTTATAAAAGAAATCGTAAAAG
* * *
1813 TTTGACAAGTTCAGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACATAAAATAAGTTTT
1 TTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT-AAATAAGTTTT
1878 T
65 T
1879 GACAAGTTCG
Statistics
Matches: 577, Mismatches: 100, Indels: 57
0.79 0.14 0.08
Matches are distributed among these distances:
206 1 0.00
207 71 0.12
208 10 0.02
209 51 0.09
210 33 0.06
214 47 0.08
215 148 0.26
216 75 0.13
217 136 0.24
218 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (213 bp):
TTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
AATTCAAAGACCAAAATATGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTTGAG
CAAGGAATGTTCGAAAAATGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTA
TAAAAGAAATCGTAAAAG
Found at i:1912 original size:63 final size:62
Alignment explanation
Indices: 1813--2002 Score: 238
Period size: 62 Copynumber: 3.0 Consensus size: 62
1803 ATCGTAAAAG
* * * *
1813 TTTGACAAGTTCAGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACATAAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACAT-AAACAAGTT
* *
1876 TTTGACAAGTTCGGAAGTTCGTCCAAGAACTAAGAGA-AAAGCAATTCTCACGTAAACAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAA-CAATTCTCACATAAACAAGTT
* * * * ** *
1938 TTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAACCAATCCTCATGTAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAACAAGTT
2000 TTT
1 TTT
2003 AATTCAGTGA
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
62 65 0.59
63 46 0.41
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (62 bp):
TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAACAAGTT
Found at i:2242 original size:341 final size:340
Alignment explanation
Indices: 1606--2247 Score: 894
Period size: 341 Copynumber: 1.9 Consensus size: 340
1596 AGTTTAAAAT
* * ** * *
1606 GTTCGAAAGTTTGTCTAAGAACAAAGAGAGAAACTGTTCTCACGTAAATATGTTTTTAATTCAAA
1 GTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATCCTCACGTAAATAAGTTTTTAATTCAAA
* * * * *
1671 GACCAAAATATTTTTCAAAATGACAAACTATTTAGACCAAATAATGTGATTTTCAGAGCAAGTAA
66 GACCAAAATATTTTACAAAATGACAAACAATTTAGACCAAATAATGCGATTTCCAGAGCAAGGAA
*** *
1736 TGTTTGGAAAATAGCTCGAAGGAATGGATCATCATGAATACTTTCAGGAACCGAAGTTATAAAAG
131 TGTTCAAAAAATAGCTCAAAGGAATGGATCATCATGAATACTTTCAGGAACCGAAGTTATAAAAG
* *
1801 AAATCGTAAAAGTTTGACAAGTTCAGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACAT
196 AAATCGTAAAAGTTTGAAAAGTTCAGATATTCGTCCAAGAACCAAGAGAGAAACAATTCTTACAT
* * *
1866 AAAATAAGTTTTTGACAAGTTCGGAAGTTCGTCCAAGAACTAAGAGAAAAGCAATTCTCACGTAA
261 AAAATAAGTTTTTGACAAGCTCAGAAGTCCGTCCAAGAACTAAGAGAAAAGCAATTCTCACGTAA
1931 ACAAGTTTTCGACAA
326 ACAAGTTTTCGACAA
* * * **
1946 GTTCGAAAGTTCGTCCAAGAACCAAGAGAGAACCAATCCTCATGTAAATAAGTTTTTAATTCAGT
1 GTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATCCTCACGTAAATAAGTTTTTAATTCAAA
* * * *
2011 GACCAAAACT-TGTTTACAGAAA-GACAAACAATTTAGACGAAATTATGCGATTTCCCGAGCATG
66 GACCAAAA-TAT-TTTACA-AAATGACAAACAATTTAGACCAAATAATGCGATTTCCAGAGCAAG
* * * * *
2074 GAATGTTCAAAAAATTGCTCAAAGGATTGGATCCTCTTGAATACTTTCAGGAACCGAAGTTATAG
128 GAATGTTCAAAAAATAGCTCAAAGGAATGGATCATCATGAATACTTTCAGGAACCGAAGTTATAA
* *
2139 AAGAAATCGTAAAAGTTTGAAAAGTAT-GGATATTCGTCCAAGAACCAAGAGAGAAATAATTCTT
193 AAGAAATCGTAAAAGTTTGAAAAGT-TCAGATATTCGTCCAAGAACCAAGAGAGAAACAATTCTT
*
2203 ACCTAAAATAAGTTTTTGACAAGCTCAGAAGTCCGTCCAAGAACT
257 ACATAAAATAAGTTTTTGACAAGCTCAGAAGTCCGTCCAAGAACT
2248 GACAGAG
Statistics
Matches: 261, Mismatches: 37, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
340 63 0.24
341 194 0.74
342 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (340 bp):
GTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATCCTCACGTAAATAAGTTTTTAATTCAAA
GACCAAAATATTTTACAAAATGACAAACAATTTAGACCAAATAATGCGATTTCCAGAGCAAGGAA
TGTTCAAAAAATAGCTCAAAGGAATGGATCATCATGAATACTTTCAGGAACCGAAGTTATAAAAG
AAATCGTAAAAGTTTGAAAAGTTCAGATATTCGTCCAAGAACCAAGAGAGAAACAATTCTTACAT
AAAATAAGTTTTTGACAAGCTCAGAAGTCCGTCCAAGAACTAAGAGAAAAGCAATTCTCACGTAA
ACAAGTTTTCGACAA
Done.