Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012564.1 Kokia drynarioides strain JFW-HI SEQ_127573, 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: 115861
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:13937 original size:20 final size:20
Alignment explanation
Indices: 13904--13942 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13894 TTAATATACT
* *
13904 TTTTTTAGATTTTTTTTTAA
1 TTTTTAAGAATTTTTTTTAA
13924 TTTTTAAGAATTTTTTTTA
1 TTTTTAAGAATTTTTTTTA
13943 GAAATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTAAGAATTTTTTTTAA
Found at i:14096 original size:20 final size:20
Alignment explanation
Indices: 14073--14110 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14063 GAATTTTCAT
14073 AACTTGTATCGATTTTTTGC
1 AACTTGTATCGATTTTTTGC
*
14093 AACTTGTATCTATTTTTT
1 AACTTGTATCGATTTTTT
14111 AGTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (20 bp):
AACTTGTATCGATTTTTTGC
Found at i:19859 original size:21 final size:23
Alignment explanation
Indices: 19824--19865 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
19814 CGAATTTGTA
*
19824 TCTTGAATTTAAA-GGTTTAGTG
1 TCTTGAATGTAAAGGGTTTAGTG
19846 TCTTGAA-GTAAAGGGTTTAG
1 TCTTGAATGTAAAGGGTTTAG
19866 AGTTTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (23 bp):
TCTTGAATGTAAAGGGTTTAGTG
Found at i:31568 original size:4 final size:4
Alignment explanation
Indices: 31559--31593 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
31549 AGGAAAAGGA
31559 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTG
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTG
31594 ATGCACTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (4 bp):
TTGT
Found at i:51398 original size:11 final size:12
Alignment explanation
Indices: 51373--51404 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
51363 ATATTAAATT
51373 AAATATTTTTAA
1 AAATATTTTTAA
51385 AAATATTTTTAA
1 AAATATTTTTAA
51397 AAATATTT
1 AAATATTT
51405 CTTTCTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATATTTTTAA
Found at i:52378 original size:16 final size:16
Alignment explanation
Indices: 52359--52396 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
52349 AATGTTTACT
*
52359 ATTTTTTAATTTAATA
1 ATTTTTTAACTTAATA
*
52375 ATTTTGTAACTTAATA
1 ATTTTTTAACTTAATA
52391 ATTTTT
1 ATTTTT
52397 GAAGATTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTTTTAACTTAATA
Found at i:54431 original size:42 final size:42
Alignment explanation
Indices: 54370--54453 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
54360 TGCTGAGTTA
* *
54370 GGTAAAGATGAGAAATTTGAGGCAGATGGTGGTCAGGAACCG
1 GGTAAAGATGAGAAATTTGAGGCAGATGGTAGCCAGGAACCG
* *
54412 GGTAAAGTTGAGAATTTTGAGGCAGATGGTAGCCAGGAACCG
1 GGTAAAGATGAGAAATTTGAGGCAGATGGTAGCCAGGAACCG
54454 CCTACTAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.37, T:0.20
Consensus pattern (42 bp):
GGTAAAGATGAGAAATTTGAGGCAGATGGTAGCCAGGAACCG
Found at i:59813 original size:29 final size:27
Alignment explanation
Indices: 59771--59824 Score: 90
Period size: 29 Copynumber: 1.9 Consensus size: 27
59761 TAGAAAAGGT
59771 GAACACTCAATTAATAGATCATAATTTTC
1 GAACACTCAATTAA-AG-TCATAATTTTC
59800 GAACACTCAATTAAAGTCATAATTT
1 GAACACTCAATTAAAGTCATAATTT
59825 GAGATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 9 0.36
28 2 0.08
29 14 0.56
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (27 bp):
GAACACTCAATTAAAGTCATAATTTTC
Found at i:59876 original size:64 final size:66
Alignment explanation
Indices: 59775--59904 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 66
59765 AAAGGTGAAC
* * * *
59775 ACTCAATTAATAGATCATAATTTTCGAACACTCAATT-A-AAGTCATAATTTGAGATTTTTAAAT
1 ACTCAATCAATAGATCATAATTTTCGAACACCCAATTAACAAGTCATAACTTGAAATTTTTAAAT
59838 T
66 T
* *
59839 ACTCAATCAGTAGATCATAATTTTCGAACACCCAATTAACAAGTTATAACTTGAAATTTTTAAAT
1 ACTCAATCAATAGATCATAATTTTCGAACACCCAATTAACAAGTCATAACTTGAAATTTTTAAAT
59904 T
66 T
59905 TCATATATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 34 0.59
65 1 0.02
66 23 0.40
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.37
Consensus pattern (66 bp):
ACTCAATCAATAGATCATAATTTTCGAACACCCAATTAACAAGTCATAACTTGAAATTTTTAAAT
T
Found at i:65026 original size:130 final size:134
Alignment explanation
Indices: 64874--65140 Score: 371
Period size: 141 Copynumber: 2.0 Consensus size: 134
64864 TAGCTGGACT
*
64874 TTTTTTCTTCATCCCTCTCTTTTATG-T-T-TG-TATATATATGTGCATGTTTATGACCCTGATG
1 TTTTTTCTTCATCCCTCTCTTTTATGCTGTACGCTATATATATGTGCATGTTTATGACCCTGATG
* * *
64935 ATGGCGGCAATAGTGGTTCTATGTGAATGTGATACATTCATACATAAGTTCTTTCCTTCTGCAAT
66 ATGGCGGCAATAGTGGTTCTATGTGAATGTGATACATGCATACACAAGTTCTGTCCTTCTGCAAT
65000 GACA
131 GACA
*
65004 TTTTTTCTTCATCCCTCTCTTTTATGCTGGTACACGCCCAATCTATATATGTGCATGTTTATGAC
1 TTTTTTCTTCATCCCTCTCTTTTATGCT-GT--ACG--C--TATATATATGTGCATGTTTATGAC
* * *
65069 CCTGATGATGGCTGCAATAGTGGTTCTATGTGAATGTGATACATGCATACGCAATTTCTGTCCTT
59 CCTGATGATGGCGGCAATAGTGGTTCTATGTGAATGTGATACATGCATACACAAGTTCTGTCCTT
65134 CTGCAAT
124 CTGCAAT
65141 TATGTGCATT
Statistics
Matches: 118, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
130 26 0.22
131 1 0.01
133 1 0.01
136 1 0.01
141 89 0.75
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (134 bp):
TTTTTTCTTCATCCCTCTCTTTTATGCTGTACGCTATATATATGTGCATGTTTATGACCCTGATG
ATGGCGGCAATAGTGGTTCTATGTGAATGTGATACATGCATACACAAGTTCTGTCCTTCTGCAAT
GACA
Found at i:67844 original size:26 final size:27
Alignment explanation
Indices: 67806--67865 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
67796 CCTGTGTGGT
* *
67806 TCATTTCATGTTTTGTACTTT-TTTT-A
1 TCATTTGAGGTTTTGTA-TTTGTTTTGA
67832 TCATTTGAGGTTTTGTATTTGTTTTGA
1 TCATTTGAGGTTTTGTATTTGTTTTGA
*
67859 TCTTTTG
1 TCATTTG
67866 TGTTATGCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 3 0.10
26 19 0.66
27 7 0.24
ACGTcount: A:0.13, C:0.08, G:0.15, T:0.63
Consensus pattern (27 bp):
TCATTTGAGGTTTTGTATTTGTTTTGA
Found at i:73386 original size:22 final size:22
Alignment explanation
Indices: 73357--73399 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
73347 TGCATAAAAG
73357 AATTAGATAAA-TAGATGTCTA
1 AATTAGATAAATTAGATGTCTA
73378 AATTGAGATAAATTTAGATGTC
1 AATT-AGATAAA-TTAGATGTC
73400 CATTTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
24 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (22 bp):
AATTAGATAAATTAGATGTCTA
Found at i:79280 original size:19 final size:19
Alignment explanation
Indices: 79256--79294 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
79246 CACTGAGTAG
79256 TTAAAGACTCTAATGATTA
1 TTAAAGACTCTAATGATTA
*
79275 TTAAAGGCTCTAATGATTA
1 TTAAAGACTCTAATGATTA
79294 T
1 T
79295 CCATAGTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (19 bp):
TTAAAGACTCTAATGATTA
Found at i:86045 original size:17 final size:17
Alignment explanation
Indices: 86023--86055 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
86013 TGTATTTACT
86023 AATAATTAAT-ATAAAAA
1 AATAA-TAATAATAAAAA
86040 AATAATAATAATAAAA
1 AATAATAATAATAAAA
86056 TTAAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAATAATAAAAA
Found at i:89285 original size:14 final size:14
Alignment explanation
Indices: 89266--89295 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
89256 TTAAGTTTTA
*
89266 TATTTTTTTTTGTT
1 TATTTTTTATTGTT
89280 TATTTTTTATTGTT
1 TATTTTTTATTGTT
89294 TA
1 TA
89296 ATAAGTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (14 bp):
TATTTTTTATTGTT
Found at i:90704 original size:2 final size:2
Alignment explanation
Indices: 90699--90740 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
90689 AAAGAGTTAA
90699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90741 TTCTATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93338 original size:24 final size:26
Alignment explanation
Indices: 93311--93358 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
93301 AGAGAAATGT
93311 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
93335 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
93359 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:93452 original size:23 final size:22
Alignment explanation
Indices: 93433--93542 Score: 105
Period size: 23 Copynumber: 4.9 Consensus size: 22
93423 TTACTGTTCA
*
93433 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCTTACTGATT
*
93455 CGCACT-TCGTGTGCCTACTGATTT
1 -GCACTGT-GTGTGCTTACTGA-TT
* * * * *
93479 GCGCTATGTGCGCCTAATGATT
1 GCACTGTGTGTGCTTACTGATT
*
93501 GCACTGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCTTACT-GATT
93524 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCTTACTG
93543 TTTCCCAGCA
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
22 18 0.25
23 52 0.71
24 3 0.04
ACGTcount: A:0.13, C:0.23, G:0.27, T:0.37
Consensus pattern (22 bp):
GCACTGTGTGTGCTTACTGATT
Found at i:107494 original size:22 final size:22
Alignment explanation
Indices: 107451--107494 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
107441 TTTGCTACTG
* *
107451 TTTATTGTCATTTTGATGTTAT
1 TTTATTGTCATTGTGATATTAT
*
107473 TTTATTGTCATTGTGCTATTAT
1 TTTATTGTCATTGTGATATTAT
107495 ATTGTTATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.07, G:0.14, T:0.61
Consensus pattern (22 bp):
TTTATTGTCATTGTGATATTAT
Found at i:109334 original size:21 final size:21
Alignment explanation
Indices: 109310--109357 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
109300 AAAAATAAAA
*
109310 AATTAAAAAT-TTTGATAATTT
1 AATTAAAAATATTTAAT-ATTT
* *
109331 AATTAGAATTATTTAATATTT
1 AATTAAAAATATTTAATATTT
109352 AATTAA
1 AATTAA
109358 TTTAAATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
AATTAAAAATATTTAATATTT
Done.