Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002537.1 Kokia drynarioides strain JFW-HI SEQ_114717, 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: 51432
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:838 original size:3 final size:3
Alignment explanation
Indices: 830--871 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
820 TGATAGCTAC
830 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
872 TTACAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:884 original size:13 final size:13
Alignment explanation
Indices: 863--910 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
853 TAATAATAAT
863 AATAATAATTTAC
1 AATAATAATTTAC
*
876 AATATTAA-TTAC
1 AATAATAATTTAC
* * *
888 AACACTAATTTAT
1 AATAATAATTTAC
901 AATAATAATT
1 AATAATAATT
911 GAATTTCTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
AATAATAATTTAC
Found at i:1412 original size:16 final size:16
Alignment explanation
Indices: 1390--1435 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1380 CTGTTCTTCC
* *
1390 TTCTTTTGTTTCTTTT
1 TTCTTTTATTTCTTTA
* *
1406 TTTTTTTCTTTCTTTA
1 TTCTTTTATTTCTTTA
1422 TTCTTTTATTTCTT
1 TTCTTTTATTTCTT
1436 ACATATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (16 bp):
TTCTTTTATTTCTTTA
Found at i:15501 original size:9 final size:8
Alignment explanation
Indices: 15487--15529 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
15477 TTGGACATGT
15487 AATAAAATA
1 AATAAAA-A
15496 AATAAATAA
1 AATAAA-AA
*
15505 AATAGAAA
1 AATAAAAA
15513 AATAAAAA
1 AATAAAAA
15521 TAATAAAAA
1 -AATAAAAA
15530 TATTTGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 9 0.30
9 20 0.67
10 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (8 bp):
AATAAAAA
Found at i:15505 original size:13 final size:13
Alignment explanation
Indices: 15487--15519 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
15477 TTGGACATGT
15487 AATAAAATA-AATA
1 AATAAAATAGAA-A
15500 AATAAAATAGAAA
1 AATAAAATAGAAA
15513 AATAAAA
1 AATAAAA
15520 ATAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.89
14 2 0.11
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AATAAAATAGAAA
Found at i:18269 original size:22 final size:22
Alignment explanation
Indices: 18212--18258 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
18202 CGATCTGAGG
18212 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
18233 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
18255 AAAA
1 AAAA
18259 GAAATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:21469 original size:23 final size:23
Alignment explanation
Indices: 21441--21485 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21431 CCTAGCTCAC
*
21441 TAGTTCACCAGATAGTCGATTTG
1 TAGTTCACCAGATAGTCAATTTG
* *
21464 TAGTTCGCCAGTTAGTCAATTT
1 TAGTTCACCAGATAGTCAATTT
21486 ACCACTCTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (23 bp):
TAGTTCACCAGATAGTCAATTTG
Found at i:22019 original size:6 final size:6
Alignment explanation
Indices: 22008--22041 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
21998 GTCACCAATG
22008 AATGTA AATGTA AATGTA AATGTA AATGTA AATG
1 AATGTA AATGTA AATGTA AATGTA AATGTA AATG
22042 ATGTGTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (6 bp):
AATGTA
Found at i:25786 original size:18 final size:18
Alignment explanation
Indices: 25763--25800 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25753 CTAAAGTTTT
25763 ATTTTAATATAATTATAC
1 ATTTTAATATAATTATAC
* *
25781 ATTTTAATTTTATTATAC
1 ATTTTAATATAATTATAC
25799 AT
1 AT
25801 ATTTTTCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATATAATTATAC
Found at i:30648 original size:16 final size:16
Alignment explanation
Indices: 30590--30662 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
30580 CAAAATATTT
*
30590 TTAAAAATATTTAACTAA
1 TTAAAATTATTTAA-T-A
* *
30608 TTTAAAATCAGTT-ATA
1 -TTAAAATTATTTAATA
* * *
30624 TTAATATTATTTGATT
1 TTAAAATTATTTAATA
30640 TTAAAATTATTTAATA
1 TTAAAATTATTTAATA
30656 TTAAAAT
1 TTAAAAT
30663 AATACAAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
15 9 0.21
16 23 0.53
17 1 0.02
18 1 0.02
19 9 0.21
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
TTAAAATTATTTAATA
Found at i:31285 original size:2 final size:2
Alignment explanation
Indices: 31278--31304 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31268 TATAGTATGA
31278 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31305 AAATAATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43396 original size:94 final size:93
Alignment explanation
Indices: 43219--43431 Score: 232
Period size: 94 Copynumber: 2.3 Consensus size: 93
43209 CCAAAAACAA
** * * *
43219 TTAATTTTAATCCCACACCAATTAGATAGAACTCTCATGCTCACACTTTTCCTATAAATAAGTGT
1 TTAATTTTAATCCCACATTAATTAGATAGAACTCTCATGCTCACACTTTACCTATAAATAAATGA
*
43284 CAATTTATTCATTGTTTTCATTAAAAAG
66 CAATTTATTCATTATTTTCATTAAAAAG
* * * *
43312 TTAATTTTAATCCCACATTAATTAGATTA-TATTTTCATATCTCACA-TTTACCTTATAAATAAA
1 TTAATTTTAATCCCACATTAATTAGA-TAGAACTCTCAT-GCTCACACTTTACC-TATAAATAAA
* * *
43375 TGACAGTTTCTTCATTATTTTCATTACAAAG
63 TGACAATTTATTCATTATTTTCATTAAAAAG
* * * *
43406 TTAAATTTAATCTCATATTAACTAGA
1 TTAATTTTAATCCCACATTAATTAGA
43432 GAATACTTTC
Statistics
Matches: 100, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
93 35 0.35
94 65 0.65
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (93 bp):
TTAATTTTAATCCCACATTAATTAGATAGAACTCTCATGCTCACACTTTACCTATAAATAAATGA
CAATTTATTCATTATTTTCATTAAAAAG
Found at i:44063 original size:189 final size:190
Alignment explanation
Indices: 43743--44163 Score: 657
Period size: 189 Copynumber: 2.2 Consensus size: 190
43733 TTCATTAAAA
* * **
43743 ATTAAAAAGTTAATTTTAATCTCTATTAACTAGAGAATACTCTCACTGCGGACAGTTACATACTC
1 ATTAAAAAGTTAATTTTAATCTCCATTAACTAGAGAATACTCCCACCACGGACAGTTACATACTC
* * * * *
43808 ATACTTACCTTACAAATAAGTGTCAATTTATTAATCATTTTCATTAAAAAGTTTATTTCAATCCC
66 ACACTTACCCTACAAATAACTGTCAATTTATTAACCATTTTCATTAAAAAGTTCATTTCAATCCC
43873 ACATTGACTCATATATTACATTTACCATATAAATAAGTAA-CAATTTTTT-CATTATTTTC
131 ACATTGACTCATATATTACATTTACCATATAAATAAGTAATC-ATTTTTTCCATTATTTTC
* *
43932 ATTAAAAAGTTAATTTTAATCTCCATTAACTAGAGAATACTCCCACCATGGACAGTTACATGCTC
1 ATTAAAAAGTTAATTTTAATCTCCATTAACTAGAGAATACTCCCACCACGGACAGTTACATACTC
* * *
43997 ACACTTACCCTATAACTAACTGTCAATTTATTCACCATTTTCATTAAAAAGTTCATTTCAATCCC
66 ACACTTACCCTACAAATAACTGTCAATTTATTAACCATTTTCATTAAAAAGTTCATTTCAATCCC
*
44062 ACATTGACTCATATCTTACATTTACCATATAAATAAGTAATCATTTTTTCCATTATTTTC
131 ACATTGACTCATATATTACATTTACCATATAAATAAGTAATCATTTTTTCCATTATTTTC
** *
44122 ATTAAAAAGTTAATTTTAATCGACATTAACTAGAGAGTACTC
1 ATTAAAAAGTTAATTTTAATCTCCATTAACTAGAGAATACTC
44164 TCATAACTCA
Statistics
Matches: 212, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
189 162 0.76
190 50 0.24
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.38
Consensus pattern (190 bp):
ATTAAAAAGTTAATTTTAATCTCCATTAACTAGAGAATACTCCCACCACGGACAGTTACATACTC
ACACTTACCCTACAAATAACTGTCAATTTATTAACCATTTTCATTAAAAAGTTCATTTCAATCCC
ACATTGACTCATATATTACATTTACCATATAAATAAGTAATCATTTTTTCCATTATTTTC
Found at i:44533 original size:69 final size:69
Alignment explanation
Indices: 44405--44582 Score: 194
Period size: 69 Copynumber: 2.6 Consensus size: 69
44395 ATAAGTGACA
* * *
44405 ATTTTTTCACTATTTTCGATTAAAAAATTTAATTTTAATCCCACGTTAATTAGAAAATATGCTTA
1 ATTTCTTCACTATTTTC-ATTAAAAAA-TTAATTTTAATCCCACATTAACTAGAAAATATGCTTA
*
44470 TAGCTC
64 TAACTC
* * * * * * **
44476 ATTTGTTCACCATTTTTATTAAAAAATTAATTTTATTCCCACATTGACTAGAGAATATTTTTATA
1 ATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCCCACATTAACTAGAAAATATGCTTATA
44541 ACTC
66 ACTC
* * * *
44545 ACTTCTTCATTATTTTCATTAAAAAGTTATTTTTAATC
1 ATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATC
44583 TGAAATTAAA
Statistics
Matches: 88, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
69 65 0.74
70 9 0.10
71 14 0.16
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (69 bp):
ATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCCCACATTAACTAGAAAATATGCTTATA
ACTC
Found at i:44785 original size:37 final size:37
Alignment explanation
Indices: 44743--44813 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
44733 GAAAGAAAGC
44743 TTATAGTTTAAAGTTATTTATT-TATTATTGATATGAT
1 TTATAGTTTAAAGTTATTT-TTATATTATTGATATGAT
*
44780 TTATAGTTTAAATTTATTTTTATATTATTGATAT
1 TTATAGTTTAAAGTTATTTTTATATTATTGATAT
44814 TATTGGTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 2 0.06
37 30 0.94
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (37 bp):
TTATAGTTTAAAGTTATTTTTATATTATTGATATGAT
Found at i:50389 original size:46 final size:46
Alignment explanation
Indices: 50334--50427 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
50324 TATATTTTTT
50334 ATTTATCATGCACTTAGTTTTCAAGTATTTGGATTATTTATTATTA
1 ATTTATCATGCACTTAGTTTTCAAGTATTTGGATTATTTATTATTA
50380 ATTTATCATGCACTTAGTTTTCAAGTATTTGGATTATTTATTATTA
1 ATTTATCATGCACTTAGTTTTCAAGTATTTGGATTATTTATTATTA
50426 AT
1 AT
50428 CAATACATCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.52
Consensus pattern (46 bp):
ATTTATCATGCACTTAGTTTTCAAGTATTTGGATTATTTATTATTA
Found at i:50481 original size:27 final size:27
Alignment explanation
Indices: 50443--50499 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
50433 CATCCATCAT
50443 TTACTAAGATTTTTACGTGTGTGGTGA
1 TTACTAAGATTTTTACGTGTGTGGTGA
*
50470 TTACTAAGATTTTTATGTGTGTGGTGA
1 TTACTAAGATTTTTACGTGTGTGGTGA
50497 TTA
1 TTA
50500 ATAATAACGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (27 bp):
TTACTAAGATTTTTACGTGTGTGGTGA
Found at i:51402 original size:4 final size:4
Alignment explanation
Indices: 51393--51428 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
51383 AAATAAACGG
*
51393 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAA
51429 GGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:51412 original size:13 final size:13
Alignment explanation
Indices: 51394--51421 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
51384 AATAAACGGG
51394 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
51407 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
51420 AA
1 AA
51422 GGAAGAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Done.