Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008454.1 Kokia drynarioides strain JFW-HI SEQ_123129, 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: 16888
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:10120 original size:487 final size:483
Alignment explanation
Indices: 9085--10122 Score: 1675
Period size: 487 Copynumber: 2.1 Consensus size: 483
9075 TGTTTATCGT
* * * *
9085 ACTGAGGTAAAACTTAAATGATGCAGGATGTAGTTCAAGAGAAGAATGGTCTTGCTAAAAAGCTG
1 ACTGAGGTAAAACTTAAATGATGCAGGAAGTAGCTCAAGAGAAGAATGATCTTGCTGAAAAGCTG
*
9150 AGGACCACCGAAGCTGATAAGAACAGATTCGTTGAAGAATTGAGAAGATGCACTTCAGAAGTTGA
66 AGGACCACCGAAGCTGATAAAAACAGATTCGTTGAAGAATTGAGAAGATGCACTTCAGAAGTTGA
9215 AACTCAAAAAGCAGAACAGTCACTTTCAAATGAAGTCCAGAGGTTGAAGCAAGAACTCAAGCAGA
131 AACTCAAAAAGCAGAACAGTCACTTTCAAATGAAGTCCAGAGGTTGAAGCAAGAACTCAAGCAGA
* *
9280 TCAAAAGAGAGAAACAGGAGAAGGAAGAGGAAATTGGACGCTGTAAGAACTATAATGATGAGCTG
196 TCAAAAGAGAGAAACAGGAGAAGGAAGAGGAAATTGGACGCTGCAAAAACTATAATGATGAGCTG
*
9345 AAAGTGAAGCTGAAAAGTTTGCAGGTTTGTTTCTTCTTACTTTCTCTGGGTCCTAGTTATGATAA
261 AAAGTAAAGCTGAAAAGTTTGCAGGTTTGTTTCTTCTTACTTTCTCTGGGTCCTAGTTATGATAA
* ** * *
9410 TGGTTCTTTCTACCATGAATCTAAAACTTCACATTCAGTTCAATTTTGTTTTGCATCTGACCTGG
326 TGGTTCTTGCTACCATGAATCTAAAACTTCACATTCAACTCAATTTTGTTTTGCATCCGACCCGG
9475 TTGTCCTTGCTATAGATTATCCTCGCAGAAGGACAAAAGCCTCTATTGGCTGTAAAATGTTTCCA
391 TTGTCCTTGC-ATAGATTATCCTCGCAGAAGGACAAAAGCCTCTATTGGCTGTAAAATGTTTCCA
* *
9540 ACTTCCCTTTGCCTTTGAGGAGTCATCTT
455 ACTGCCCTTTGCCTTTGAGGAGTCATCTA
* *
9569 ACTGAGGTGAAAACTTAGATGATGCAGGAAGTAGCTCAAGAGAAGTATGATCTTGCTG-AAAGCT
1 ACTGAGGT-AAAACTTAAATGATGCAGGAAGTAGCTCAAGAGAAGAATGATCTTGCTGAAAAGCT
* * * * *
9633 GCGGACCACTGAAGCTGATAAAAATAGATTTGTTGAAGAATTGAGAAGATGCAGTTCAGAAGTTG
65 GAGGACCACCGAAGCTGATAAAAACAGATTCGTTGAAGAATTGAGAAGATGCACTTCAGAAGTTG
* * * * *
9698 AAGCTCAAAAGGCAGAACAACAGTCACTTTCAAATGAAGTCCAGATGTTGAAGCAAGAACTTAGG
130 AAACTCAAAAAGCAG---AACAGTCACTTTCAAATGAAGTCCAGAGGTTGAAGCAAGAACTCAAG
* *
9763 CAGATCGAAAGAGAGAAACAGGAGAAGGAAGAGGAAATTGGACGCTGCAAAAACTATAATTATGA
192 CAGATCAAAAGAGAGAAACAGGAGAAGGAAGAGGAAATTGGACGCTGCAAAAACTATAATGATGA
* * *
9828 GCTGGAAGTAAAGTTGAATAGTTTGCAGGTTTGTTTCTTCTTACTTTCTCTGGGTCCTAGTTATG
257 GCTGAAAGTAAAGCTGAAAAGTTTGCAGGTTTGTTTCTTCTTACTTTCTCTGGGTCCTAGTTATG
*
9893 ATAATGGTTCTTGCTACCATGAATTTAAAACTTCACATTCAACTCAATTTTGTTTTGCATCCGAC
322 ATAATGGTTCTTGCTACCATGAATCTAAAACTTCACATTCAACTCAATTTTGTTTTGCATCCGAC
*
9958 CCGGTTGTCCTTGC-TAGATTATCTTCGCAGAAGGACAAAAGCCTCTATTGGCTGTAAAATGTTT
387 CCGGTTGTCCTTGCATAGATTATCCTCGCAGAAGGACAAAAGCCTCTATTGGCTGTAAAATGTTT
10022 CCAACTGCCCTTTGCCTTTGAGGAGTCATCTA
452 CCAACTGCCCTTTGCCTTTGAGGAGTCATCTA
* *
10054 ACTGAGGTCAAAAACTTAAATGATGCAGGAAGTGGCTCAAGAGAGGAATGATCTTGCTGAAAAGC
1 ACTGAGGT--AAAACTTAAATGATGCAGGAAGTAGCTCAAGAGAAGAATGATCTTGCTGAAAAGC
10119 TGAG
64 TGAG
10123 AAGCATCGAG
Statistics
Matches: 508, Mismatches: 40, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
484 86 0.17
485 130 0.26
486 45 0.09
487 247 0.49
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (483 bp):
ACTGAGGTAAAACTTAAATGATGCAGGAAGTAGCTCAAGAGAAGAATGATCTTGCTGAAAAGCTG
AGGACCACCGAAGCTGATAAAAACAGATTCGTTGAAGAATTGAGAAGATGCACTTCAGAAGTTGA
AACTCAAAAAGCAGAACAGTCACTTTCAAATGAAGTCCAGAGGTTGAAGCAAGAACTCAAGCAGA
TCAAAAGAGAGAAACAGGAGAAGGAAGAGGAAATTGGACGCTGCAAAAACTATAATGATGAGCTG
AAAGTAAAGCTGAAAAGTTTGCAGGTTTGTTTCTTCTTACTTTCTCTGGGTCCTAGTTATGATAA
TGGTTCTTGCTACCATGAATCTAAAACTTCACATTCAACTCAATTTTGTTTTGCATCCGACCCGG
TTGTCCTTGCATAGATTATCCTCGCAGAAGGACAAAAGCCTCTATTGGCTGTAAAATGTTTCCAA
CTGCCCTTTGCCTTTGAGGAGTCATCTA
Found at i:12266 original size:248 final size:247
Alignment explanation
Indices: 11841--12921 Score: 1776
Period size: 248 Copynumber: 4.4 Consensus size: 247
11831 TACTTTCGTA
* * * *
11841 TAATCTTAAAAGATTGCCAAAGGGTACAAGAAAGAGGAAAGAATGGGGTCTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
* * * * *
11906 TGGTATTGATCTTTACATATGTCCTCACAGTGATGCCATAATCACCGTACTTGTAGAACGTGGTT
66 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTT
11971 TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
131 TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
* *
12036 CCTGGGATGCATCTAT-AGGATTTCTGATGCAAATATCAATTCATACTTTATTG
196 ACTGGGATGCATCT-TGAGGATTTCTGATGTAAATATCAATTCATACTTT-TTG
12089 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
* **
12154 TCGTATTGATCTTTACATATGTCCTCGCAGTTCTGCCATAATCACCATACTTGCAAAACATGGTT
66 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTT
* **
12219 TCTTCAAGGGTTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAAAG
131 TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
* *
12284 ACTGGGATGCATCTTGAGGATTTTTTATGTAAATATCAATTCATAC---TTG
196 ACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAATTCATACTTTTTG
*
12333 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGAAAAGAGTGGGGTTTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
* * *
12398 TGGTATTGATCTTTACATATGTCCTCGCAGTGCTGCCATAATCAACATACTTGCCAAACATGGTT
66 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTT
*
12463 TCTTCAAGGGCTGGGATGAATGAGG-AGGTTGGTTGAGAAGGAACATGAAGATGGTCATATAGTG
131 TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
* * *
12527 GCTGGGATGCATCTTGAGGATTTCTGATGTAAATACCACTTCATACTTTCTTG
196 ACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAATTCATACTTT-TTG
*
12580 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAAGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
* * *
12645 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGTCATAATAACCATACTTGCAAGACATGGTT
66 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTT
* *
12710 TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGACAAGGAACATGAAGATTGTCATATAGTG
131 TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
*
12775 ACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAAGTCATACTTTTTTG
196 ACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAATTCATAC-TTTTTG
*
12828 TAAACTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
12893 TGGTATTGATCTTTACATATGTCCTCGCA
66 TGGTATTGATCTTTACATATGTCCTCGCA
12922 TCACCAAACT
Statistics
Matches: 777, Mismatches: 49, Indels: 14
0.93 0.06 0.02
Matches are distributed among these distances:
243 77 0.10
244 152 0.20
247 151 0.19
248 394 0.51
249 3 0.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (247 bp):
TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTT
TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
ACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAATTCATACTTTTTG
Found at i:12770 original size:491 final size:492
Alignment explanation
Indices: 11841--12921 Score: 1783
Period size: 491 Copynumber: 2.2 Consensus size: 492
11831 TACTTTCGTA
* * *
11841 TAATCTTAAAAGATTGCCAAAGGGTACAAGAAAGAGGAAAGAATGGGGTCTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAG-GGAAAGAGTGGGGTTTGCTCAACTCTCACC
* * * * *
11906 TGGTATTGATCTTTACATATGTCCTCACAGTGATGCCATAATCACCGTACTTGTAGAACGTGGTT
65 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCAACATACTTGCAGAACATGGTT
11971 TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
130 TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
*
12036 CCTGGGATGCATCTATAGGATTTCTGATGCAAATATCAATTCATACTTTATTGTAATCTTAACAG
195 CCTGGGATGCATCTATAGGATTTCTGATGCAAATACCAATTCATACTTTATTGTAATCTTAACAG
*
12101 ATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTCGTATTGATCT
260 ATTGCCAAAGGGTACAAGAAAAGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTCGTATTGATCT
** * *
12166 TTACATATGTCCTCGCAGTTCTGCCATAATCACCATACTTGCAAAACATGGTTTCTTCAAGGGTT
325 TTACATATGTCCTCGCAGTGATGCCATAATAACCATACTTGCAAAACATGGTTTCTTCAAGGGCT
12231 GGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAAAGACTGGGATGCAT
390 GGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAAAGACTGGGATGCAT
* * *
12296 CTTGAGGATTTTTTATGTAAATATCAATTCATAC-TTG
455 CTTGAGGATTTCTGATGTAAATATCAAGTCATACTTTG
12333 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGAAAAGAGTGGGGTTTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGG-AAAGAGTGGGGTTTGCTCAACTCTCACC
*
12398 TGGTATTGATCTTTACATATGTCCTCGCAGTGCTGCCATAATCAACATACTTGCCA-AACATGGT
65 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCAACATACTTG-CAGAACATGGT
*
12462 TTCTTCAAGGGCTGGGATGAATGAGG-AGGTTGGTTGAGAAGGAACATGAAGATGGTCATATAGT
129 TTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGT
* * * *
12526 GGCTGGGATGCATCT-TGAGGATTTCTGATGTAAATACCACTTCATACTTTCTTGTAATCTTAAC
194 GCCTGGGATGCATCTAT-AGGATTTCTGATGCAAATACCAATTCATACTTTATTGTAATCTTAAC
*
12590 AGATTGCCAAAGGGTACAAGAAAAGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTGGTATTGAT
258 AGATTGCCAAAGGGTACAAGAAAAGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTCGTATTGAT
* *
12655 CTTTACATATGTCCTCGCAGTGATGTCATAATAACCATACTTGCAAGACATGGTTTCTTCAAGGG
323 CTTTACATATGTCCTCGCAGTGATGCCATAATAACCATACTTGCAAAACATGGTTTCTTCAAGGG
* * **
12720 CTGGGATGAATGAGGTAGGTTGGTTGACAAGGAACATGAAGATTGTCATATAGTGACTGGGATGC
388 CTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAAAGACTGGGATGC
12785 ATCTTGAGGATTTCTGATGTAAATATCAAGTCATACTTTTTTG
453 ATCTTGAGGATTTCTGATGTAAATATCAAGTCATAC---TTTG
*
12828 TAAACTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAA-GGGAAAGAGTGGGGTTTGCTCAACTCTCACC
12893 TGGTATTGATCTTTACATATGTCCTCGCA
65 TGGTATTGATCTTTACATATGTCCTCGCA
12922 TCACCAAACT
Statistics
Matches: 550, Mismatches: 31, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
490 1 0.00
491 312 0.57
492 141 0.26
493 1 0.00
495 92 0.17
496 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (492 bp):
TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGAAAGAGTGGGGTTTGCTCAACTCTCACCT
GGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCAACATACTTGCAGAACATGGTTT
CTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTGC
CTGGGATGCATCTATAGGATTTCTGATGCAAATACCAATTCATACTTTATTGTAATCTTAACAGA
TTGCCAAAGGGTACAAGAAAAGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTCGTATTGATCTT
TACATATGTCCTCGCAGTGATGCCATAATAACCATACTTGCAAAACATGGTTTCTTCAAGGGCTG
GGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAAAGACTGGGATGCATC
TTGAGGATTTCTGATGTAAATATCAAGTCATACTTTG
Done.