Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007805.1 Kokia drynarioides strain JFW-HI SEQ_122440, 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, 863
Length: 1439
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Found at i:398 original size:221 final size:221
Alignment explanation
Indices: 1--1439 Score: 1934
Period size: 221 Copynumber: 6.4 Consensus size: 221
*
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAAGAGGGATATTATCCCTTTCCAA
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
* * *
66 TAGTTTTATGCCACACCAACAATTTCAACCTGTATTTCTGGATTTTAATTTTAA-TTTATTTTTT
66 TAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTTA-TTTTT
* *
130 TCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAATTATTAGAAAAGGG
130 TCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGG
* *
195 ATACAGATGACGTGGTGTCACTGTTTC
195 ACACAAATGACGTGGTGTCACTGTTTC
* * * * * * *
222 ATTCAATCCTTTTCCGTTGAAGAAGAGAAAGGACTGTATTAAACAGTGAAATTATCACTTTGCAA
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
* * *
287 TAGTTTTATGCCTCATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTATTTTTATTTTTT
66 TAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTTATTTTTT
* * * *
352 CAGGATGAAAATGTTAAAATTAAGAATGAAAAAAATGATGTGGCGTAAAACTATAAGAAAAGGGA
131 CAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGGA
* *
417 CACAAATGACGTGGTGTCAGTATTTC
196 CACAAATGACGTGGTGTCACTGTTTC
*
443 ATTCAAT-CTGTTTCCATTGAAG-A-AGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCA
1 ATTCAATCCT-TTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCA
* * * *
505 ATAGTTTTATGCCACACCAACAATTTCATCCTAAATTTCAGGATTTTAATTTGAATTTGATATTT
65 ATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTTATTTTT
* * * * *
570 TCAGGATGAAAAGGATGAAATTAAGAATAAAAATACTGATGCGGCGTAAAACTATTGGAAAAGGG
130 TCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGG
* * *
635 ACACAAATGAAGTTGTGTCACTTTTTC
195 ACACAAATGACGTGGTGTCACTGTTTC
* * *
662 GTTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAAGGATATTATCCCTTTCCAA
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
* ** *
727 TAGTTTTATGCCACAGCAACAATTTCATTTTGAATTTCAGGATTTTAATTTTATTTTTATTTTTT
66 TAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTTATTTTTT
* * *
792 CAGGATGAAAATGTTGAAATTAAGAATCAAAATACTGATGTGGAGTAAAACTATTGGAAAAGGGA
131 CAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGGA
*
857 CACAAATGACGTTGTGTCACTGTTTC
196 CACAAATGACGTGGTGTCACTGTTTC
*
883 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTTTCCCTTTCCAA
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
* ** * * *
948 TAGTTTTATTCCACGTCATCAATTTCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTT
66 TAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTTATTTTTT
* * *
1013 AAGGATGAAAATGTTGAAATTAAGAATGAAAATATTGATGTGGCGTAAAACAATTAGAAAAGGGA
131 CAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGGA
1078 CACAAATGACGTGGTGTCACTGTTTTATTC
196 CACAAATGACGTGGTGTCACTG---T-TTC
* *
1108 AATCCTTTTCCATTTTATTGAATCATTTTCCATTGAAGAAGAGAAAGAATTGTATGAAACAGGGA
1 -A-----TT-C---------AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGA
**
1173 TATTATCCCTTTCTTATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAAT
50 TATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAAT
* * * **
1238 TTTAATTTGATTTTTTCAGGATTAAAATGTTTAAATTAAGAATGAAAATACAAATGTGGCGTAAA
115 TTTAATTTTATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAA
* * ** * *
1303 ACAATTGGAAAAAAGACAC-AATAACGTGGTGTTACTGTTTC
180 ACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTC
* * *
1344 ATTCAATCTTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAAGAGGGATATTTTCCCTTTCCAA
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
** *
1409 TAGTTTTATGCCACGTCATCAATTTCATCCT
66 TAGTTTTATGCCACACCAACAATTTCATCCT
Statistics
Matches: 1073, Mismatches: 120, Indels: 51
0.86 0.10 0.04
Matches are distributed among these distances:
219 188 0.18
220 88 0.08
221 586 0.55
222 4 0.00
224 1 0.00
225 3 0.00
226 1 0.00
229 1 0.00
230 2 0.00
231 2 0.00
232 1 0.00
235 1 0.00
236 3 0.00
237 1 0.00
240 16 0.01
241 175 0.16
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (221 bp):
ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
TAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTTATTTTTT
CAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGGA
CACAAATGACGTGGTGTCACTGTTTC
Found at i:854 original size:440 final size:442
Alignment explanation
Indices: 1--1439 Score: 1972
Period size: 440 Copynumber: 3.2 Consensus size: 442
*
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAAGAGGGATATTATCCCTTTCCAA
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
* * *
66 TAGTTTTATGCCACACCAACAATTTCAACCTGTATTTCTGGATTTTAATTTTAATTT-ATTTTTT
66 TAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGA-TTTTT
* *
130 TCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAATTATTAGAAAAGGG
130 TCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGG
* * * * * *
195 ATACAGATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCGTTGAAGAAGAGAAAGGACTGTA
195 ACACAAATGACGTGGTGTCACTTTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTA
* * * * * *
260 TTAAAC-AGTGAAATTATCACTTTGCAATAGTTTTATGCCTCATCAACAATTTCATCCTGAATTT
260 TGAAACAAG-GATATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTT
* *
324 CAGGATTTTAATTTTATTTTTATTTTTTCAGGATGAAAATGTTAAAATTAAGAATGAAAAAAATG
324 CAGGATTTTAATTTTATTTTTATTTTTTCAGGATGAAAATGTTAAAATTAAGAATGAAAATACTG
** * *
389 ATGTGGCGTAAAACTATAAGAAAAGGGACACAAATGACGTGGTGTCAGTATTTC
389 ATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTC
*
443 ATTCAAT-CTGTTTCCATTGAAG-A-AGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCA
1 ATTCAATCCT-TTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCA
* * *
505 ATAGTTTTATGCCACACCAACAATTTCATCCTAAATTTCAGGATTTTAATTTGAATTTGATATTT
65 ATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTT
* * * * *
570 TCAGGATGAAAAGGATGAAATTAAGAATAAAAATACTGATGCGGCGTAAAACTATTGGAAAAGGG
130 TCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGG
* * *
635 ACACAAATGAAGTTGTGTCACTTTTTCGTTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTA
195 ACACAAATGACGTGGTGTCACTTTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTA
* **
700 TGAAACAAGGATATTATCCCTTTCCAATAGTTTTATGCCACAGCAACAATTTCATTTTGAATTTC
260 TGAAACAAGGATATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTC
* *
765 AGGATTTTAATTTTATTTTTATTTTTTCAGGATGAAAATGTTGAAATTAAGAATCAAAATACTGA
325 AGGATTTTAATTTTATTTTTATTTTTTCAGGATGAAAATGTTAAAATTAAGAATGAAAATACTGA
* *
830 TGTGGAGTAAAACTATTGGAAAAGGGACACAAATGACGTTGTGTCACTGTTTC
390 TGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTC
*
883 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTTTCCCTTTCCAA
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
* ** * *
948 TAGTTTTATTCCACGTCATCAATTTCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTT
66 TAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTT
* * *
1013 AAGGATGAAAATGTTGAAATTAAGAATGAAAATATTGATGTGGCGTAAAACAATTAGAAAAGGGA
131 CAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGGA
1078 CACAAATGACGTGGTGTCACTGTTTTATTCAATCCTTTTCCATTTTATTGAATCATTTTCCATTG
196 CACAAATGACGTGGTGTCAC---TTT-TTC-A-----TT-C---------AATCATTTTCCATTG
* * **
1143 AAGAAGAGAAAGAATTGTATGAAACAGGGATATTATCCCTTTCTTATAGTTTTATGCCACACCAA
241 AAGAAGAGAAAGGATTGTATGAAACAAGGATATTATCCCTTTCCAATAGTTTTATGCCACACCAA
* * * *
1208 CAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATTAAAATGTTTAAA
306 CAATTTCATCCTGAATTTCAGGATTTTAATTTTATTTTTATTTTTTCAGGATGAAAATGTTAAAA
** * ** * *
1273 TTAAGAATGAAAATACAAATGTGGCGTAAAACAATTGGAAAAAAGACAC-AATAACGTGGTGTTA
371 TTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACGTGGTGTCA
1337 CTGTTTC
436 CTGTTTC
* * *
1344 ATTCAATCTTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAAGAGGGATATTTTCCCTTTCCAA
1 ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
** *
1409 TAGTTTTATGCCACGTCATCAATTTCATCCT
66 TAGTTTTATGCCACACCAACAATTTCATCCT
Statistics
Matches: 884, Mismatches: 87, Indels: 33
0.88 0.09 0.03
Matches are distributed among these distances:
440 389 0.44
441 9 0.01
442 189 0.21
445 3 0.00
446 3 0.00
452 2 0.00
453 1 0.00
461 112 0.13
462 176 0.20
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (442 bp):
ATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAA
TAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTT
CAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAGAAAAGGGA
CACAAATGACGTGGTGTCACTTTTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTAT
GAAACAAGGATATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAATTTCA
GGATTTTAATTTTATTTTTATTTTTTCAGGATGAAAATGTTAAAATTAAGAATGAAAATACTGAT
GTGGCGTAAAACTATTGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTC
Found at i:1035 original size:21 final size:21
Alignment explanation
Indices: 1011--1050 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1001 ATTTGATTTT
* *
1011 TTAAGGATGAAAATGTTGAAA
1 TTAAGAATGAAAATATTGAAA
1032 TTAAGAATGAAAATATTGA
1 TTAAGAATGAAAATATTGA
1051 TGTGGCGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (21 bp):
TTAAGAATGAAAATATTGAAA
Found at i:1125 original size:20 final size:20
Alignment explanation
Indices: 1100--1141 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1090 GGTGTCACTG
*
1100 TTTTATTCAATCCTTTTCCA
1 TTTTATTCAATCATTTTCCA
*
1120 TTTTATTGAATCATTTTCCA
1 TTTTATTCAATCATTTTCCA
1140 TT
1 TT
1142 GAAGAAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTATTCAATCATTTTCCA
Found at i:1323 original size:241 final size:240
Alignment explanation
Indices: 887--1361 Score: 734
Period size: 241 Copynumber: 2.0 Consensus size: 240
877 TGTTTCATTC
* * *
887 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTTTCCCTTTCCAATAGT
1 AATCATTTTCCATTGAAGAAGAGAAAGAATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
* ** *
952 TTTATTCCACGTCATCAATTTCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTAAGG
66 TTTATGCCACACCAACAATTTCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTAAGG
*** **
1017 ATGAAAATGTTGAAATTAAGAATGAAAATATTGATGTGGCGTAAAACAATTAGAAAAGGGACACA
131 ATGAAAATGTTGAAATTAAGAATGAAAATACAAATGTGGCGTAAAACAATTAGAAAAAAGACAC-
* *
1082 AATGACGTGGTGTCACTGTTTTATTCAATCCTTTTCCATTTTATTG
195 AATAACGTGGTGTCACTGTTTCATTCAATCCTTTTCCATTTTATTG
**
1128 AATCATTTTCCATTGAAGAAGAGAAAGAATTGTATGAAACAGGGATATTATCCCTTTCTTATAGT
1 AATCATTTTCCATTGAAGAAGAGAAAGAATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
* *
1193 TTTATGCCACACCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
66 TTTATGCCACACCAACAATTTCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTAAGG
* * *
1258 ATTAAAATGTTTAAATTAAGAATGAAAATACAAATGTGGCGTAAAACAATTGGAAAAAAGACACA
131 ATGAAAATGTTGAAATTAAGAATGAAAATACAAATGTGGCGTAAAACAATTAGAAAAAAGACACA
* *
1323 ATAACGTGGTGTTACTGTTTCATTCAATCTTTTTCCATT
196 ATAACGTGGTGTCACTGTTTCATTCAATCCTTTTCCATT
1362 GAAGAAGAGA
Statistics
Matches: 211, Mismatches: 23, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
240 36 0.17
241 175 0.83
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (240 bp):
AATCATTTTCCATTGAAGAAGAGAAAGAATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
TTTATGCCACACCAACAATTTCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTAAGG
ATGAAAATGTTGAAATTAAGAATGAAAATACAAATGTGGCGTAAAACAATTAGAAAAAAGACACA
ATAACGTGGTGTCACTGTTTCATTCAATCCTTTTCCATTTTATTG
Done.