Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005400.1 Kokia drynarioides strain JFW-HI SEQ_119407, 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, 872
Length: 1454
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Found at i:157 original size:89 final size:89
Alignment explanation
Indices: 1--1058 Score: 1141
Period size: 89 Copynumber: 12.0 Consensus size: 89
** * * * * * *
1 TTTAGGTATTAAATAAAACCACGTTACTATACCCTTTTTAATAGTGTCATTCATAAAAAAATTCA
1 TTTAGGTATTAAATAAAATTACGTTACTTTACCTTTTTTAGTAGTGTCATTCATAATAGAATACA
*
66 TTTCCAAACATAAAATAAATATAT
66 TTTCCAAACATAAAATAAAGATAT
* * * *
90 TTTAGGTATTAAATAAAATTCCGTTGCTTTACTTTTTTTAGTATTGTCATTCATAATAGAATACA
1 TTTAGGTATTAAATAAAATTACGTTACTTTACCTTTTTTAGTAGTGTCATTCATAATAGAATACA
155 TTTCCAAACATAAAATAAAGACT-T
66 TTTCCAAACATAAAATAAAGA-TAT
* * * * * * * *
179 TTTAGGAATTAAAGAAAATTACGTTACTTCACTTTTTTTAGTAGTGTTATTTATATTAGAATACG
1 TTTAGGTATTAAATAAAATTACGTTACTTTACCTTTTTTAGTAGTGTCATTCATAATAGAATACA
*
244 TTTACAAACAT-AAA-AAA-ATAT
66 TTTCCAAACATAAAATAAAGATAT
** * * * * *
265 TTTAGGTATTAAATAAAACCACGTTACTATAACC-TTTTTAATAGTGTCATTCATAAAAAAATTC
1 TTTAGGTATTAAATAAAATTACGTTACT-TTACCTTTTTTAGTAGTGTCATTCATAATAGAATAC
329 ATTTCCAAACATAAAATAAAGATAT
65 ATTTCCAAACATAAAATAAAGATAT
* *
354 TTTAGGTATTAAATAAAATTACGTT-TTTTCACCTTTTTTAGTAGTGTCATTTATAATAGAATAC
1 TTTAGGTATTAAATAAAATTACGTTACTTT-ACCTTTTTTAGTAGTGTCATTCATAATAGAATAC
*
418 ATTTTCAAACATAAAATAAAGACT-T
65 ATTTCCAAACATAAAATAAAGA-TAT
* * * * * * * *
443 TTTAGGAAATAAAGAAAATTACGTTACTTTACTTTTTTTAGTAGTGTTATTTATATTAGAATACG
1 TTTAGGTATTAAATAAAATTACGTTACTTTACCTTTTTTAGTAGTGTCATTCATAATAGAATACA
* *
508 TTTACAAACAT-AAA-AAA-ACAT
66 TTTCCAAACATAAAATAAAGATAT
* * * * * *
529 TTTAGGTAATAAATAAAATTCCGTTGCTTTACTTTTTTTAGTATTGTCATTCATAATATAATACA
1 TTTAGGTATTAAATAAAATTACGTTACTTTACCTTTTTTAGTAGTGTCATTCATAATAGAATACA
594 TTTCCAAACATAAAATAAAGACT-T
66 TTTCCAAACATAAAATAAAGA-TAT
* * * * * * * * * *
618 TTTAGGAAATAAAGAAAATTACGTTACTTCACTTTTTTTAATAGTGTTATTTATATTAGAATACG
1 TTTAGGTATTAAATAAAATTACGTTACTTTACCTTTTTTAGTAGTGTCATTCATAATAGAATACA
* *
683 TTTACAAACAT-AAA-AAA-ACAT
66 TTTCCAAACATAAAATAAAGATAT
** * * * * * *
704 TTTAGGTATTAAATAAAACCACGTTACTATACCCTTTTTAATAGTGTCATTCATAAAAAAATTCA
1 TTTAGGTATTAAATAAAATTACGTTACTTTACCTTTTTTAGTAGTGTCATTCATAATAGAATACA
769 TTTCCAAACATAAAATAAAGATAT
66 TTTCCAAACATAAAATAAAGATAT
* *
793 TTTAGGTATTAAATAAAATTACGTT-TTTTCACCTTTTTTAGTAGTGTCATTTATAATAGAATAC
1 TTTAGGTATTAAATAAAATTACGTTACTTT-ACCTTTTTTAGTAGTGTCATTCATAATAGAATAC
* *
857 ATTTCTAAACATAAAATAAAAACT-T
65 ATTTCCAAACATAAAATAAAGA-TAT
* * *
882 TTTAGGTATTAAA-AAAATTACGTT-TTTTCACCTTTTTTAGTAGTGTCATTTATAATATAATAC
1 TTTAGGTATTAAATAAAATTACGTTACTTT-ACCTTTTTTAGTAGTGTCATTCATAATAGAATAC
*
945 ATTTCCAAAAAT-AAA-AAA-ATAT
65 ATTTCCAAACATAAAATAAAGATAT
** * * * * *
967 TTTAGGTATTAAATAAAACCACATTACTTCACCTTTTTTAGTAATGTCATTCATAATATAATTCA
1 TTTAGGTATTAAATAAAATTACGTTACTTTACCTTTTTTAGTAGTGTCATTCATAATAGAATACA
*
1032 TTTCCAAACATAAAATAAAGACAT
66 TTTCCAAACATAAAATAAAGATAT
1056 TTT
1 TTT
1059 GTAACACCCT
Statistics
Matches: 814, Mismatches: 128, Indels: 54
0.82 0.13 0.05
Matches are distributed among these distances:
84 1 0.00
85 16 0.02
86 240 0.29
87 30 0.04
88 86 0.11
89 435 0.53
90 6 0.01
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (89 bp):
TTTAGGTATTAAATAAAATTACGTTACTTTACCTTTTTTAGTAGTGTCATTCATAATAGAATACA
TTTCCAAACATAAAATAAAGATAT
Found at i:315 original size:175 final size:175
Alignment explanation
Indices: 1--1058 Score: 1089
Period size: 175 Copynumber: 6.0 Consensus size: 175
** * * * * * *
1 TTTAGGTATTAAATAAAACCACGTTACTAT-ACCCTTTTTAATAGTGTCATTCATAAAAAAATTC
1 TTTAGGTATTAAATAAAATTACGTTACT-TCACCTTTTTTAGTAGTGTCATTTATAATAGAATAC
* * *
65 ATTTCCAAACATAAAATAAATATATTTTAGGTATTAAATAAAATTC-CGTTGCTTTACTTTTTTT
65 ATTTCCAAACAT-AAA-AAA-ATATTTTAGGTATTAAATAAAA-TCACGTTACTTCACTCTTTTT
* *
129 AGTATTGTCATTCATAATAGAATACATTTCCAAACATAAAATAAAGACTT
126 AGTAGTGTCATTCATAATAGAATACATTTCCAAACATAAAATAAAGACAT
* * * * * *
179 TTTAGGAATTAAAGAAAATTACGTTACTTCACTTTTTTTAGTAGTGTTATTTATATTAGAATACG
1 TTTAGGTATTAAATAAAATTACGTTACTTCACCTTTTTTAGTAGTGTCATTTATAATAGAATACA
* * * *
244 TTTACAAACATAAAAAAATATTTTAGGTATTAAATAAAACCACGTTACTATAAC-CTTTTTAATA
66 TTTCCAAACATAAAAAAATATTTTAGGTATTAAATAAAATCACGTTACT-TCACTCTTTTTAGTA
* * * *
308 GTGTCATTCATAAAAAAATTCATTTCCAAACATAAAATAAAGATAT
130 GTGTCATTCATAATAGAATACATTTCCAAACATAAAATAAAGACAT
**
354 TTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTAGTAGTGTCATTTATAATAGAATACA
1 TTTAGGTATTAAATAAAATTACGTTACTTCACCTTTTTTAGTAGTGTCATTTATAATAGAATACA
* * * * * * * *
419 TTTTCAAACATAAAATAAAGACTTTTTAGGAAATAAAGAAAATTACGTTACTTTACTTTTTTTAG
66 TTTCCAAACATAAAA-AAATA--TTTTAGGTATTAAATAAAATCACGTTACTTCACTCTTTTTAG
* * * * *
484 TAGTGTTATTTATATTAGAATACGTTTACAAACAT-AAA-AAA-ACAT
128 TAGTGTCATTCATAATAGAATACATTTCCAAACATAAAATAAAGACAT
* * * * * * * *
529 TTTAGGTAATAAATAAAATTCCGTTGCTTTACTTTTTTTAGTATTGTCATTCATAATATAATACA
1 TTTAGGTATTAAATAAAATTACGTTACTTCACCTTTTTTAGTAGTGTCATTTATAATAGAATACA
* * * * * * *
594 TTTCCAAACATAAAATAAAGACTTTTTAGGAAATAAAGAAAATTACGTTACTTCACTTTTTTTAA
66 TTTCCAAACATAAAA-AAATA--TTTTAGGTATTAAATAAAATCACGTTACTTCACTCTTTTTAG
* * * * *
659 TAGTGTTATTTATATTAGAATACGTTTACAAACAT-AAA-AAA-ACAT
128 TAGTGTCATTCATAATAGAATACATTTCCAAACATAAAATAAAGACAT
** * * * * * *
704 TTTAGGTATTAAATAAAACCACGTTACTAT-ACCCTTTTTAATAGTGTCATTCATAAAAAAATTC
1 TTTAGGTATTAAATAAAATTACGTTACT-TCACCTTTTTTAGTAGTGTCATTTATAATAGAATAC
* **
768 ATTTCCAAACATAAAATAAAGATATTTTAGGTATTAAATAAAATTACGTTTTTTCAC-CTTTTTT
65 ATTTCCAAACAT-AAA-AAA-ATATTTTAGGTATTAAATAAAATCACGTTACTTCACTC-TTTTT
* * * *
832 AGTAGTGTCATTTATAATAGAATACATTTCTAAACATAAAATAAAAACTT
126 AGTAGTGTCATTCATAATAGAATACATTTCCAAACATAAAATAAAGACAT
** *
882 TTTAGGTATTAAA-AAAATTACGTTTTTTCACCTTTTTTAGTAGTGTCATTTATAATATAATACA
1 TTTAGGTATTAAATAAAATTACGTTACTTCACCTTTTTTAGTAGTGTCATTTATAATAGAATACA
* * *
946 TTTCCAAAAATAAAAAAATATTTTAGGTATTAAATAAAACCACATTACTTCAC-CTTTTTTAGTA
66 TTTCCAAACATAAAAAAATATTTTAGGTATTAAATAAAATCACGTTACTTCACTC-TTTTTAGTA
* * *
1010 ATGTCATTCATAATATAATTCATTTCCAAACATAAAATAAAGACAT
130 GTGTCATTCATAATAGAATACATTTCCAAACATAAAATAAAGACAT
1056 TTT
1 TTT
1059 GTAACACCCT
Statistics
Matches: 750, Mismatches: 114, Indels: 36
0.83 0.13 0.04
Matches are distributed among these distances:
174 85 0.11
175 442 0.59
176 26 0.03
177 65 0.09
178 132 0.18
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (175 bp):
TTTAGGTATTAAATAAAATTACGTTACTTCACCTTTTTTAGTAGTGTCATTTATAATAGAATACA
TTTCCAAACATAAAAAAATATTTTAGGTATTAAATAAAATCACGTTACTTCACTCTTTTTAGTAG
TGTCATTCATAATAGAATACATTTCCAAACATAAAATAAAGACAT
Found at i:471 original size:264 final size:263
Alignment explanation
Indices: 1--1046 Score: 1207
Period size: 264 Copynumber: 4.0 Consensus size: 263
* *
1 TTTAGGTATTAAATAAAACCACGTTACTATACCCTTTTTAATAGTGTCATTCATAAAAAAATTCA
1 TTTAGGTATTAAATAAAACCACGTTACTATAACCTTTTTAATAGTGTCATTCATAAAAAAATACA
* * * *
66 TTTCCAAACATAAAATAAATA-TATTTTAGGTATTAAATAAAATTCCGTTGCTTT-ACTTTTTTT
66 TTTCCAAACATAAAATAAAGACT-TTTTAGGTATTAAATAAAATTACGTT-TTTTCACCTTTTTT
* *
129 AGTATTGTCATTCATAATAGAATACATTTCCAAACATAAAATAAAGACTTTTTAGGAATTAAAGA
129 AGTAGTGTCATTTATAATAGAATACATTTCCAAACATAAAA-AAAGACTTTTTAGGAATTAAAGA
** * * * * *
194 AAATTACGTTACTTCACTTTTTTTAGTAGTGTTATTTATATTAGAATACGTTTACAAACATAAAA
193 AAACCACGTTACTTCACCTTTTTTAGTAGTGTCATTCATAATAGAATACATTTACAAACATAAAA
259 AAATAT
258 AAATAT
*
265 TTTAGGTATTAAATAAAACCACGTTACTATAACCTTTTTAATAGTGTCATTCATAAAAAAATTCA
1 TTTAGGTATTAAATAAAACCACGTTACTATAACCTTTTTAATAGTGTCATTCATAAAAAAATACA
330 TTTCCAAACATAAAATAAAGA-TATTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTA
66 TTTCCAAACATAAAATAAAGACT-TTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTA
* *
394 GTAGTGTCATTTATAATAGAATACATTTTCAAACATAAAATAAAGACTTTTTAGGAAATAAAGAA
130 GTAGTGTCATTTATAATAGAATACATTTCCAAACATAAAA-AAAGACTTTTTAGGAATTAAAGAA
** * * * * * *
459 AATTACGTTACTTTACTTTTTTTAGTAGTGTTATTTATATTAGAATACGTTTACAAACATAAAAA
194 AACCACGTTACTTCACCTTTTTTAGTAGTGTCATTCATAATAGAATACATTTACAAACATAAAAA
*
524 AACAT
259 AATAT
* * * * * * * * *
529 TTTAGGTAATAAATAAAATTC-CGTTGCT-TTACTTTTTTTAGTATTGTCATTCATAATATAATA
1 TTTAGGTATTAAATAAAA-CCACGTTACTATAAC-CTTTTTAATAGTGTCATTCATAAAAAAATA
* * * ** *
592 CATTTCCAAACATAAAATAAAGACTTTTTAGGAAATAAAGAAAATTACGTTACTTCACTTTTTTT
64 CATTTCCAAACATAAAATAAAGACTTTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTT
* * * * * * * *
657 AATAGTGTTATTTATATTAGAATACGTTTACAAACAT-AAAAAA-ACATTTTAGGTATTAAATAA
129 AGTAGTGTCATTTATAATAGAATACATTTCCAAACATAAAAAAAGACTTTTTAGGAATTAAAGAA
* * * * * *
720 AACCACGTTACTAT-ACCCTTTTTAATAGTGTCATTCATAAAAAAATTCATTTCCAAACATAAAA
194 AACCACGTTACT-TCACCTTTTTTAGTAGTGTCATTCATAATAGAATACATTTACAAACAT-AAA
784 TAAAGATAT
257 -AAA-ATAT
** * * * * * * *
793 TTTAGGTATTAAATAAAATTACGTT-TTTTCACCTTTTTTAGTAGTGTCATTTATAATAGAATAC
1 TTTAGGTATTAAATAAAACCACGTTACTATAACC-TTTTTAATAGTGTCATTCATAAAAAAATAC
* *
857 ATTTCTAAACATAAAATAAAAACTTTTTAGGTATTAAA-AAAATTACGTTTTTTCACCTTTTTTA
65 ATTTCCAAACATAAAATAAAGACTTTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTA
* * * * *
921 GTAGTGTCATTTATAATATAATACATTTCCAAAAATAAAAAAATA--TTTTAGGTATTAAATAAA
130 GTAGTGTCATTTATAATAGAATACATTTCCAAACATAAAAAAAGACTTTTTAGGAATTAAAGAAA
* * * * *
984 ACCACATTACTTCACCTTTTTTAGTAATGTCATTCATAATATAATTCATTTCCAAACATAAAA
195 ACCACGTTACTTCACCTTTTTTAGTAGTGTCATTCATAATAGAATACATTTACAAACATAAAA
1047 TAAAGACATT
Statistics
Matches: 690, Mismatches: 78, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
261 62 0.09
262 11 0.02
263 135 0.20
264 479 0.69
265 3 0.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (263 bp):
TTTAGGTATTAAATAAAACCACGTTACTATAACCTTTTTAATAGTGTCATTCATAAAAAAATACA
TTTCCAAACATAAAATAAAGACTTTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTAG
TAGTGTCATTTATAATAGAATACATTTCCAAACATAAAAAAAGACTTTTTAGGAATTAAAGAAAA
CCACGTTACTTCACCTTTTTTAGTAGTGTCATTCATAATAGAATACATTTACAAACATAAAAAAA
TAT
Found at i:919 original size:439 final size:438
Alignment explanation
Indices: 21--1058 Score: 1670
Period size: 439 Copynumber: 2.4 Consensus size: 438
11 AAATAAAACC
* * * * * * * *
21 ACGTTACTATACCCTTTTTAATAGTGTCATTCATAAAAAAATTCATTTCCAAACATAAAATAAAT
1 ACGTTACTTTA-CTTTTTTAGTAGTGTCATTTATAATAGAATACATTTACAAACAT-AAA-AAA-
*
86 ATATTTTAGGTATTAAATAAAATTCCGTTGCTTTACTTTTTTTAGTATTGTCATTCATAATAGAA
62 ATATTTTAGGTATTAAATAAAATTCCGTTGCTTTACTTTTTTTAGTATTGTCATTCATAATATAA
*
151 TACATTTCCAAACATAAAATAAAGACTTTTTAGGAATTAAAGAAAATTACGTTACTTCACTTTTT
127 TACATTTCCAAACATAAAATAAAGACTTTTTAGGAAATAAAGAAAATTACGTTACTTCACTTTTT
* *
216 TTAGTAGTGTTATTTATATTAGAATACGTTTACAAACATAAAAAAATATTTTAGGTATTAAATAA
192 TTAATAGTGTTATTTATATTAGAATACGTTTACAAACATAAAAAAACATTTTAGGTATTAAATAA
281 AACCACGTTACTATAACCTTTTTAATAGTGTCATTCATAAAAAAATTCATTTCCAAACATAAAAT
257 AACCACGTTACTATAACCTTTTTAATAGTGTCATTCATAAAAAAATTCATTTCCAAACATAAAAT
346 AAAGATATTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTAGTAGTGTCATTTATAAT
322 AAAGATATTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTAGTAGTGTCATTTATAAT
*
411 AGAATACATTTTCAAACATAAAATAAAGACTTTTTAGGAAATAAAGAAAATT
387 AGAATACATTTTCAAACATAAAATAAAAACTTTTTAGGAAATAAAGAAAATT
* * * *
463 ACGTTACTTTACTTTTTTTAGTAGTGTTATTTATATTAGAATACGTTTACAAACATAAAAAAACA
1 ACGTTACTTTAC-TTTTTTAGTAGTGTCATTTATAATAGAATACATTTACAAACATAAAAAAATA
*
528 TTTTAGGTAATAAATAAAATTCCGTTGCTTTACTTTTTTTAGTATTGTCATTCATAATATAATAC
65 TTTTAGGTATTAAATAAAATTCCGTTGCTTTACTTTTTTTAGTATTGTCATTCATAATATAATAC
593 ATTTCCAAACATAAAATAAAGACTTTTTAGGAAATAAAGAAAATTACGTTACTTCACTTTTTTTA
130 ATTTCCAAACATAAAATAAAGACTTTTTAGGAAATAAAGAAAATTACGTTACTTCACTTTTTTTA
658 ATAGTGTTATTTATATTAGAATACGTTTACAAACATAAAAAAACATTTTAGGTATTAAATAAAAC
195 ATAGTGTTATTTATATTAGAATACGTTTACAAACATAAAAAAACATTTTAGGTATTAAATAAAAC
*
723 CACGTTACTATACCCTTTTTAATAGTGTCATTCATAAAAAAATTCATTTCCAAACATAAAATAAA
260 CACGTTACTATAACCTTTTTAATAGTGTCATTCATAAAAAAATTCATTTCCAAACATAAAATAAA
788 GATATTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTAGTAGTGTCATTTATAATAGA
325 GATATTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTAGTAGTGTCATTTATAATAGA
* *
853 ATACA-TTTCTAAACATAAAATAAAAACTTTTTAGGTATTAAA-AAAATT
390 ATACATTTTC-AAACATAAAATAAAAACTTTTTAGGAAATAAAGAAAATT
* * * *
901 ACGTT-TTTTCACCTTTTTTAGTAGTGTCATTTATAATATAATACATTTCCAAAAATAAAAAAAT
1 ACGTTACTTT-A-CTTTTTTAGTAGTGTCATTTATAATAGAATACATTTACAAACATAAAAAAAT
* * * * * *
965 ATTTTAGGTATTAAATAAAA-CCACATTACTTCACCTTTTTTAGTAATGTCATTCATAATATAAT
64 ATTTTAGGTATTAAATAAAATTC-CGTTGCTTTACTTTTTTTAGTATTGTCATTCATAATATAAT
* *
1029 TCATTTCCAAACATAAAATAAAGACATTTT
128 ACATTTCCAAACATAAAATAAAGACTTTTT
1059 GTAACACCCT
Statistics
Matches: 553, Mismatches: 38, Indels: 14
0.91 0.06 0.02
Matches are distributed among these distances:
437 4 0.01
438 143 0.26
439 356 0.64
440 3 0.01
441 4 0.01
442 43 0.08
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (438 bp):
ACGTTACTTTACTTTTTTAGTAGTGTCATTTATAATAGAATACATTTACAAACATAAAAAAATAT
TTTAGGTATTAAATAAAATTCCGTTGCTTTACTTTTTTTAGTATTGTCATTCATAATATAATACA
TTTCCAAACATAAAATAAAGACTTTTTAGGAAATAAAGAAAATTACGTTACTTCACTTTTTTTAA
TAGTGTTATTTATATTAGAATACGTTTACAAACATAAAAAAACATTTTAGGTATTAAATAAAACC
ACGTTACTATAACCTTTTTAATAGTGTCATTCATAAAAAAATTCATTTCCAAACATAAAATAAAG
ATATTTTAGGTATTAAATAAAATTACGTTTTTTCACCTTTTTTAGTAGTGTCATTTATAATAGAA
TACATTTTCAAACATAAAATAAAAACTTTTTAGGAAATAAAGAAAATT
Done.